CrocoBLAST:UserManual - Revision history

https://webchemwiki.biodata.ceitec.cz/index.php?action=history&feed=atom&title=CrocoBLAST%3AUserManual CrocoBLAST:UserManual - Revision history 2026-04-21T22:16:01Z Revision history for this page on the wiki MediaWiki 1.44.0 https://webchemwiki.biodata.ceitec.cz/index.php?title=CrocoBLAST:UserManual&diff=2358&oldid=prev Crina at 20:07, 8 April 2017 2017-04-08T20:07:42Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:07, 8 April 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l523">Line 523:</td> <td colspan="2" class="diff-lineno">Line 523:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''<small style="font-size:200%;">VI) Instructions for Mac OS X users</small>'''<div class="mw-collapsible-content"></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''<small style="font-size:200%;">VI) Instructions for Mac OS X users</small>'''<div class="mw-collapsible-content"></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While a native version of '''CrocoBLAST''' for Mac OS X is not available at the moment, it is possible to run CrocoBLAST on Mac OS X achieving a great speed up over the Mac OS version of BLAST+. For that, you need to install a Linux virtual machine and follow all the instructions as if you were running the command line version of CrocoBLAST on Linux.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While a native version of '''CrocoBLAST''' for Mac OS X is not available at the moment, it is possible to run CrocoBLAST on Mac OS X achieving a great speed up over the Mac OS version of BLAST+. For that, you need to install a Linux virtual machine and follow all the instructions as if you were running the command line version of CrocoBLAST on Linux.</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>There are several different virtualization solutions for creating a Linux virtual machine inside Mac OS X. We tested a free solution for CrocoBLAST on Mac OS X by running CrocoBLAST inside an Ubuntu 16.04 Linux (https://www.ubuntu.com/) virtual machine created using Oracle's <del style="font-weight: bold; text-decoration: none;">Virtual Box </del>(https://www.virtualbox.org/). Instructions for setting up a Linux virtual machine can be found in the <del style="font-weight: bold; text-decoration: none;">Virtual Box </del>user manual (http://download.virtualbox.org/virtualbox/UserManual.pdf) under the sections: "2.2 Installing on Mac OS X hosts", for installation; "1.6 Starting VirtualBox", "1.7 Creating your first virtual machine", and "1.8 Running your virtual machine", for creating and using the Linux virtual machine; and "3 Configuring virtual machines", in case you desire to use advanced features of the virtual machine.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>There are several different virtualization solutions for creating a Linux virtual machine inside Mac OS X. We tested a free solution for CrocoBLAST on Mac OS X by running CrocoBLAST inside an Ubuntu 16.04 Linux (https://www.ubuntu.com/) virtual machine created using Oracle's <ins style="font-weight: bold; text-decoration: none;">VirtualBox </ins>(https://www.virtualbox.org/). Instructions for setting up a Linux virtual machine can be found in the <ins style="font-weight: bold; text-decoration: none;">VirtualBox </ins>user manual (http://download.virtualbox.org/virtualbox/UserManual.pdf) under the sections: "2.2 Installing on Mac OS X hosts", for installation; "1.6 Starting VirtualBox", "1.7 Creating your first virtual machine", and "1.8 Running your virtual machine", for creating and using the Linux virtual machine; and "3 Configuring virtual machines", in case you desire to use advanced features of the virtual machine.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>After these steps, you may follow the regular instructions for CrocoBLAST inside the virtual machine as if you were running it on a native Linux environment.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>After these steps, you may follow the regular instructions for CrocoBLAST inside the virtual machine as if you were running it on a native Linux environment.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td></tr> </table>

Crina https://webchemwiki.biodata.ceitec.cz/index.php?title=CrocoBLAST:UserManual&diff=2357&oldid=prev Crina at 20:05, 8 April 2017 2017-04-08T20:05:29Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:05, 8 April 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l522">Line 522:</td> <td colspan="2" class="diff-lineno">Line 522:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----<div class="mw-collapsible mw-collapsed"></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----<div class="mw-collapsible mw-collapsed"></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''<small style="font-size:200%;">VI) Instructions for Mac OS X users</small>'''<div class="mw-collapsible-content"></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''<small style="font-size:200%;">VI) Instructions for Mac OS X users</small>'''<div class="mw-collapsible-content"></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>While a native version of '''CrocoBLAST''' for Mac OS X is <del style="font-weight: bold; text-decoration: none;">still </del>not available, it is possible to run CrocoBLAST on Mac OS X achieving a great speed up over the Mac OS version of BLAST+. For that, you need to install a Linux virtual machine and follow all the instructions as if you were running the command line version of CrocoBLAST on Linux.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>While a native version of '''CrocoBLAST''' for Mac OS X is not available <ins style="font-weight: bold; text-decoration: none;">at the moment</ins>, it is possible to run CrocoBLAST on Mac OS X achieving a great speed up over the Mac OS version of BLAST+. For that, you need to install a Linux virtual machine and follow all the instructions as if you were running the command line version of CrocoBLAST on Linux.</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>There are several different virtualization solutions for creating a Linux virtual machine inside Mac OS X. We tested a free solution for CrocoBLAST on Mac OS X by running CrocoBLAST inside an Ubuntu 16.04 Linux (https://www.ubuntu.com/) virtual machine created using Oracle's Virtual Box (https://www.virtualbox.org/). Instructions for <del style="font-weight: bold; text-decoration: none;">performing such setup </del>can be found in the Virtual Box user manual (http://download.virtualbox.org/virtualbox/UserManual.pdf) under the sections: "2.2 Installing on Mac OS X hosts", for installation; "1.6 Starting VirtualBox", "1.7 Creating your first virtual machine", and "1.8 Running your virtual machine", for creating and using the Linux virtual machine; and "3 Configuring virtual machines", in case you desire to use advanced features of the virtual machine.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>There are several different virtualization solutions for creating a Linux virtual machine inside Mac OS X. We tested a free solution for CrocoBLAST on Mac OS X by running CrocoBLAST inside an Ubuntu 16.04 Linux (https://www.ubuntu.com/) virtual machine created using Oracle's Virtual Box (https://www.virtualbox.org/). Instructions for <ins style="font-weight: bold; text-decoration: none;">setting up a Linux virtual machine </ins>can be found in the Virtual Box user manual (http://download.virtualbox.org/virtualbox/UserManual.pdf) under the sections: "2.2 Installing on Mac OS X hosts", for installation; "1.6 Starting VirtualBox", "1.7 Creating your first virtual machine", and "1.8 Running your virtual machine", for creating and using the Linux virtual machine; and "3 Configuring virtual machines", in case you desire to use advanced features of the virtual machine.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>After these steps, you may follow the regular instructions for CrocoBLAST inside the virtual machine as if you were running it on a native Linux environment.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>After these steps, you may follow the regular instructions for CrocoBLAST inside the virtual machine as if you were running it on a native Linux environment.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td></tr> </table>

Crina https://webchemwiki.biodata.ceitec.cz/index.php?title=CrocoBLAST:UserManual&diff=2356&oldid=prev Crina at 20:02, 8 April 2017 2017-04-08T20:02:17Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:02, 8 April 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l521">Line 521:</td> <td colspan="2" class="diff-lineno">Line 521:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----<div class="mw-collapsible mw-collapsed"></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----<div class="mw-collapsible mw-collapsed"></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>'''<small style="font-size:200%;">VI) Instructions for Mac OS users</small>'''<div class="mw-collapsible-content"></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>'''<small style="font-size:200%;">VI) Instructions for Mac OS <ins style="font-weight: bold; text-decoration: none;">X </ins>users</small>'''<div class="mw-collapsible-content"></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While a native version of '''CrocoBLAST''' for Mac OS X is still not available, it is possible to run CrocoBLAST on Mac OS X achieving a great speed up over the Mac OS version of BLAST+. For that, you need to install a Linux virtual machine and follow all the instructions as if you were running the command line version of CrocoBLAST on Linux.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While a native version of '''CrocoBLAST''' for Mac OS X is still not available, it is possible to run CrocoBLAST on Mac OS X achieving a great speed up over the Mac OS version of BLAST+. For that, you need to install a Linux virtual machine and follow all the instructions as if you were running the command line version of CrocoBLAST on Linux.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There are several different virtualization solutions for creating a Linux virtual machine inside Mac OS X. We tested a free solution for CrocoBLAST on Mac OS X by running CrocoBLAST inside an Ubuntu 16.04 Linux (https://www.ubuntu.com/) virtual machine created using Oracle's Virtual Box (https://www.virtualbox.org/). Instructions for performing such setup can be found in the Virtual Box user manual (http://download.virtualbox.org/virtualbox/UserManual.pdf) under the sections: "2.2 Installing on Mac OS X hosts", for installation; "1.6 Starting VirtualBox", "1.7 Creating your first virtual machine", and "1.8 Running your virtual machine", for creating and using the Linux virtual machine; and "3 Configuring virtual machines", in case you desire to use advanced features of the virtual machine.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There are several different virtualization solutions for creating a Linux virtual machine inside Mac OS X. We tested a free solution for CrocoBLAST on Mac OS X by running CrocoBLAST inside an Ubuntu 16.04 Linux (https://www.ubuntu.com/) virtual machine created using Oracle's Virtual Box (https://www.virtualbox.org/). Instructions for performing such setup can be found in the Virtual Box user manual (http://download.virtualbox.org/virtualbox/UserManual.pdf) under the sections: "2.2 Installing on Mac OS X hosts", for installation; "1.6 Starting VirtualBox", "1.7 Creating your first virtual machine", and "1.8 Running your virtual machine", for creating and using the Linux virtual machine; and "3 Configuring virtual machines", in case you desire to use advanced features of the virtual machine.</div></td></tr> </table>

Crina https://webchemwiki.biodata.ceitec.cz/index.php?title=CrocoBLAST:UserManual&diff=2355&oldid=prev Crina at 20:02, 8 April 2017 2017-04-08T20:02:02Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:02, 8 April 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l518">Line 518:</td> <td colspan="2" class="diff-lineno">Line 518:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>CrocoBLAST typically checks that the necessary files and permissions exist before starting the demanding BLAST calculation.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>CrocoBLAST typically checks that the necessary files and permissions exist before starting the demanding BLAST calculation.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">If you get into trouble while trying to run CrocoBLAST, please check the error messages, which are quite informative and should help you overcome the most common issues you are likely to encounter. If you experience further issues, please contact us and describe the problem in detail.</ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">If you get into trouble while trying to run CrocoBLAST, please check the error messages, which are quite informative and should help you overcome the most common issues you are likely to encounter. If you experience further issues, please contact us and describe the problem in detail.</del></div></td><td colspan="2" class="diff-side-added"></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----<div class="mw-collapsible mw-collapsed"></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----<div class="mw-collapsible mw-collapsed"></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''<small style="font-size:200%;">VI) Instructions for Mac OS users</small>'''<div class="mw-collapsible-content"></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''<small style="font-size:200%;">VI) Instructions for Mac OS users</small>'''<div class="mw-collapsible-content"></div></td></tr> </table>

Crina https://webchemwiki.biodata.ceitec.cz/index.php?title=CrocoBLAST:UserManual&diff=2354&oldid=prev Crina at 20:01, 8 April 2017 2017-04-08T20:01:37Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:01, 8 April 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l518">Line 518:</td> <td colspan="2" class="diff-lineno">Line 518:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>CrocoBLAST typically checks that the necessary files and permissions exist before starting the demanding BLAST calculation.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>CrocoBLAST typically checks that the necessary files and permissions exist before starting the demanding BLAST calculation.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></div></div></ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>If you get into trouble while trying to run CrocoBLAST, please check the error messages, which are quite informative and should help you overcome the most common issues you are likely to encounter. If you experience further issues, please contact us and describe the problem in detail.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>If you get into trouble while trying to run CrocoBLAST, please check the error messages, which are quite informative and should help you overcome the most common issues you are likely to encounter. If you experience further issues, please contact us and describe the problem in detail.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----<div class="mw-collapsible mw-collapsed"></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----<div class="mw-collapsible mw-collapsed"></div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l524">Line 524:</td> <td colspan="2" class="diff-lineno">Line 525:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There are several different virtualization solutions for creating a Linux virtual machine inside Mac OS X. We tested a free solution for CrocoBLAST on Mac OS X by running CrocoBLAST inside an Ubuntu 16.04 Linux (https://www.ubuntu.com/) virtual machine created using Oracle's Virtual Box (https://www.virtualbox.org/). Instructions for performing such setup can be found in the Virtual Box user manual (http://download.virtualbox.org/virtualbox/UserManual.pdf) under the sections: "2.2 Installing on Mac OS X hosts", for installation; "1.6 Starting VirtualBox", "1.7 Creating your first virtual machine", and "1.8 Running your virtual machine", for creating and using the Linux virtual machine; and "3 Configuring virtual machines", in case you desire to use advanced features of the virtual machine.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There are several different virtualization solutions for creating a Linux virtual machine inside Mac OS X. We tested a free solution for CrocoBLAST on Mac OS X by running CrocoBLAST inside an Ubuntu 16.04 Linux (https://www.ubuntu.com/) virtual machine created using Oracle's Virtual Box (https://www.virtualbox.org/). Instructions for performing such setup can be found in the Virtual Box user manual (http://download.virtualbox.org/virtualbox/UserManual.pdf) under the sections: "2.2 Installing on Mac OS X hosts", for installation; "1.6 Starting VirtualBox", "1.7 Creating your first virtual machine", and "1.8 Running your virtual machine", for creating and using the Linux virtual machine; and "3 Configuring virtual machines", in case you desire to use advanced features of the virtual machine.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>After these steps, you may follow the regular instructions for CrocoBLAST inside the virtual machine as if you were running it on a native Linux environment.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>After these steps, you may follow the regular instructions for CrocoBLAST inside the virtual machine as if you were running it on a native Linux environment.</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></div></div></del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td></tr> </table>

Crina https://webchemwiki.biodata.ceitec.cz/index.php?title=CrocoBLAST:UserManual&diff=2353&oldid=prev Crina at 20:00, 8 April 2017 2017-04-08T20:00:55Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:00, 8 April 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l524">Line 524:</td> <td colspan="2" class="diff-lineno">Line 524:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There are several different virtualization solutions for creating a Linux virtual machine inside Mac OS X. We tested a free solution for CrocoBLAST on Mac OS X by running CrocoBLAST inside an Ubuntu 16.04 Linux (https://www.ubuntu.com/) virtual machine created using Oracle's Virtual Box (https://www.virtualbox.org/). Instructions for performing such setup can be found in the Virtual Box user manual (http://download.virtualbox.org/virtualbox/UserManual.pdf) under the sections: "2.2 Installing on Mac OS X hosts", for installation; "1.6 Starting VirtualBox", "1.7 Creating your first virtual machine", and "1.8 Running your virtual machine", for creating and using the Linux virtual machine; and "3 Configuring virtual machines", in case you desire to use advanced features of the virtual machine.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There are several different virtualization solutions for creating a Linux virtual machine inside Mac OS X. We tested a free solution for CrocoBLAST on Mac OS X by running CrocoBLAST inside an Ubuntu 16.04 Linux (https://www.ubuntu.com/) virtual machine created using Oracle's Virtual Box (https://www.virtualbox.org/). Instructions for performing such setup can be found in the Virtual Box user manual (http://download.virtualbox.org/virtualbox/UserManual.pdf) under the sections: "2.2 Installing on Mac OS X hosts", for installation; "1.6 Starting VirtualBox", "1.7 Creating your first virtual machine", and "1.8 Running your virtual machine", for creating and using the Linux virtual machine; and "3 Configuring virtual machines", in case you desire to use advanced features of the virtual machine.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>After these steps, you may follow the regular instructions for CrocoBLAST inside the virtual machine as if you were running it on a native Linux environment.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>After these steps, you may follow the regular instructions for CrocoBLAST inside the virtual machine as if you were running it on a native Linux environment.</div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></div></div></ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td></tr> </table>

Crina https://webchemwiki.biodata.ceitec.cz/index.php?title=CrocoBLAST:UserManual&diff=2352&oldid=prev Crina at 20:00, 8 April 2017 2017-04-08T20:00:19Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:00, 8 April 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l521">Line 521:</td> <td colspan="2" class="diff-lineno">Line 521:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----<div class="mw-collapsible mw-collapsed"></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----<div class="mw-collapsible mw-collapsed"></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''<small style="font-size:200%;">VI) Instructions for Mac OS users</small>'''<div class="mw-collapsible-content"></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''<small style="font-size:200%;">VI) Instructions for Mac OS users</small>'''<div class="mw-collapsible-content"></div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>While a native version of '''CrocoBLAST''' for Mac OS X is still not available, it is possible to run CrocoBLAST on Mac OS X achieving a great speed over the Mac OS version of BLAST+. For that, you need to install a Linux virtual machine and follow all the instructions as if you were running the command line version of CrocoBLAST on Linux.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>While a native version of '''CrocoBLAST''' for Mac OS X is still not available, it is possible to run CrocoBLAST on Mac OS X achieving a great speed <ins style="font-weight: bold; text-decoration: none;">up </ins>over the Mac OS version of BLAST+. For that, you need to install a Linux virtual machine and follow all the instructions as if you were running the command line version of CrocoBLAST on Linux.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There are several different virtualization solutions for creating a Linux virtual machine inside Mac OS X. We tested a free solution for CrocoBLAST on Mac OS X by running CrocoBLAST inside an Ubuntu 16.04 Linux (https://www.ubuntu.com/) virtual machine created using Oracle's Virtual Box (https://www.virtualbox.org/). Instructions for performing such setup can be found in the Virtual Box user manual (http://download.virtualbox.org/virtualbox/UserManual.pdf) under the sections: "2.2 Installing on Mac OS X hosts", for installation; "1.6 Starting VirtualBox", "1.7 Creating your first virtual machine", and "1.8 Running your virtual machine", for creating and using the Linux virtual machine; and "3 Configuring virtual machines", in case you desire to use advanced features of the virtual machine.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There are several different virtualization solutions for creating a Linux virtual machine inside Mac OS X. We tested a free solution for CrocoBLAST on Mac OS X by running CrocoBLAST inside an Ubuntu 16.04 Linux (https://www.ubuntu.com/) virtual machine created using Oracle's Virtual Box (https://www.virtualbox.org/). Instructions for performing such setup can be found in the Virtual Box user manual (http://download.virtualbox.org/virtualbox/UserManual.pdf) under the sections: "2.2 Installing on Mac OS X hosts", for installation; "1.6 Starting VirtualBox", "1.7 Creating your first virtual machine", and "1.8 Running your virtual machine", for creating and using the Linux virtual machine; and "3 Configuring virtual machines", in case you desire to use advanced features of the virtual machine.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>After these steps, you may follow the regular instructions for CrocoBLAST inside the virtual machine as if you were running it on a native Linux environment.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>After these steps, you may follow the regular instructions for CrocoBLAST inside the virtual machine as if you were running it on a native Linux environment.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td></tr> </table>

Crina https://webchemwiki.biodata.ceitec.cz/index.php?title=CrocoBLAST:UserManual&diff=2351&oldid=prev Crina at 19:58, 8 April 2017 2017-04-08T19:58:47Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:58, 8 April 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l519">Line 519:</td> <td colspan="2" class="diff-lineno">Line 519:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>If you get into trouble while trying to run CrocoBLAST, please check the error messages, which are quite informative and should help you overcome the most common issues you are likely to encounter. If you experience further issues, please contact us and describe the problem in detail.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>If you get into trouble while trying to run CrocoBLAST, please check the error messages, which are quite informative and should help you overcome the most common issues you are likely to encounter. If you experience further issues, please contact us and describe the problem in detail.</div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">----<div class="mw-collapsible mw-collapsed"></ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">'''<small style="font-size:200%;">VI) Instructions for Mac OS users</small>'''<div class="mw-collapsible-content"></ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">While a native version of '''CrocoBLAST''' for Mac OS X is still not available, it is possible to run CrocoBLAST on Mac OS X achieving a great speed over the Mac OS version of BLAST+. For that, you need to install a Linux virtual machine and follow all the instructions as if you were running the command line version of CrocoBLAST on Linux.</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">There are several different virtualization solutions for creating a Linux virtual machine inside Mac OS X. We tested a free solution for CrocoBLAST on Mac OS X by running CrocoBLAST inside an Ubuntu 16.04 Linux (https://www.ubuntu.com/) virtual machine created using Oracle's Virtual Box (https://www.virtualbox.org/). Instructions for performing such setup can be found in the Virtual Box user manual (http://download.virtualbox.org/virtualbox/UserManual.pdf) under the sections: "2.2 Installing on Mac OS X hosts", for installation; "1.6 Starting VirtualBox", "1.7 Creating your first virtual machine", and "1.8 Running your virtual machine", for creating and using the Linux virtual machine; and "3 Configuring virtual machines", in case you desire to use advanced features of the virtual machine.</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">After these steps, you may follow the regular instructions for CrocoBLAST inside the virtual machine as if you were running it on a native Linux environment.</ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div></div></div></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td></tr> </table>

Crina https://webchemwiki.biodata.ceitec.cz/index.php?title=CrocoBLAST:UserManual&diff=2350&oldid=prev Crina: /* 1. Software requirements */ 2017-04-08T19:12:18Z

<p><span class="autocomment">1. Software requirements</span></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:12, 8 April 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l505">Line 505:</td> <td colspan="2" class="diff-lineno">Line 505:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''CrocoBLAST''' is free to use within the conditions of its license, and has been available for download since July 2016 at http://webchem.ncbr.muni.cz/Platform/App/CrocoBLAST. There is no login requirement for downloading or running '''CrocoBLAST'''. For running the graphical user interface, simply double click it. For running the command line utility, please open a command line prompt (terminal in Linux, cmd in Windows).</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''CrocoBLAST''' is free to use within the conditions of its license, and has been available for download since July 2016 at http://webchem.ncbr.muni.cz/Platform/App/CrocoBLAST. There is no login requirement for downloading or running '''CrocoBLAST'''. For running the graphical user interface, simply double click it. For running the command line utility, please open a command line prompt (terminal in Linux, cmd in Windows).</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=1. Software requirements=</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=1. Software requirements=</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>'''CrocoBLAST''' runs on Windows and Linux<del style="font-weight: bold; text-decoration: none;">, and all results </del>are <del style="font-weight: bold; text-decoration: none;">provided </del>in the <del style="font-weight: bold; text-decoration: none;">regular </del>BLAST output <del style="font-weight: bold; text-decoration: none;">format</del>. Once you download the "zip" with all necessary '''CrocoBLAST''' files, all you need to do is unzip it to the desired location. As CrocoBLAST works as a wrapper for BLAST, you will need to have BLAST available on your computer before you can run CrocoBLAST. If you don't already have BLAST, please [https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download get the latest version from the NCBI website]. No further requirements exist for running the command line utility of '''CrocoBLAST''', or inspecting the results. In Windows, downloading files from the NCBI server requires PowerShell, which ships automatically with Windows 7 and newer, and can be installed on Windows XP and Vista. The graphical user interface requires Java 8, which is likely already installed on your computer. If not, please visit https://java.com/en/download/.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>'''CrocoBLAST''' runs on Windows and Linux<ins style="font-weight: bold; text-decoration: none;">. Mac OS users can use CrocoBLAST by creating a Linux virtual machine in their Mac computer. Instructions on how to run CrocoBLAST on Mac </ins>are <ins style="font-weight: bold; text-decoration: none;">found </ins>in <ins style="font-weight: bold; text-decoration: none;">chapter VI of this manual. CrocoBLAST is able to produce its output on 3 of </ins>the BLAST output <ins style="font-weight: bold; text-decoration: none;">formats</ins>. Once you download the "zip" with all necessary '''CrocoBLAST''' files, all you need to do is unzip it to the desired location. As CrocoBLAST works as a wrapper for BLAST, you will need to have BLAST available on your computer before you can run CrocoBLAST. If you don't already have BLAST, please [https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download get the latest version from the NCBI website]. No further requirements exist for running the command line utility of '''CrocoBLAST''', or inspecting the results. In Windows, downloading files from the NCBI server requires PowerShell, which ships automatically with Windows 7 and newer, and can be installed on Windows XP and Vista. The graphical user interface requires Java 8, which is likely already installed on your computer. If not, please visit https://java.com/en/download/.</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=2. Hardware requirements=</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=2. Hardware requirements=</div></td></tr> </table>

Crina https://webchemwiki.biodata.ceitec.cz/index.php?title=CrocoBLAST:UserManual&diff=2349&oldid=prev Crina: /* 1. Software requirements */ 2017-04-08T19:05:55Z

<p><span class="autocomment">1. Software requirements</span></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 19:05, 8 April 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l506">Line 506:</td> <td colspan="2" class="diff-lineno">Line 506:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=1. Software requirements=</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=1. Software requirements=</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''CrocoBLAST''' runs on Windows and Linux, and all results are provided in the regular BLAST output format. Once you download the "zip" with all necessary '''CrocoBLAST''' files, all you need to do is unzip it to the desired location. As CrocoBLAST works as a wrapper for BLAST, you will need to have BLAST available on your computer before you can run CrocoBLAST. If you don't already have BLAST, please [https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download get the latest version from the NCBI website]. No further requirements exist for running the command line utility of '''CrocoBLAST''', or inspecting the results. In Windows, downloading files from the NCBI server requires PowerShell, which ships automatically with Windows 7 and newer, and can be installed on Windows XP and Vista. The graphical user interface requires Java 8, which is likely already installed on your computer. If not, please visit https://java.com/en/download/.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>'''CrocoBLAST''' runs on Windows and Linux, and all results are provided in the regular BLAST output format. Once you download the "zip" with all necessary '''CrocoBLAST''' files, all you need to do is unzip it to the desired location. As CrocoBLAST works as a wrapper for BLAST, you will need to have BLAST available on your computer before you can run CrocoBLAST. If you don't already have BLAST, please [https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download get the latest version from the NCBI website]. No further requirements exist for running the command line utility of '''CrocoBLAST''', or inspecting the results. In Windows, downloading files from the NCBI server requires PowerShell, which ships automatically with Windows 7 and newer, and can be installed on Windows XP and Vista. The graphical user interface requires Java 8, which is likely already installed on your computer. If not, please visit https://java.com/en/download/.</div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=2. Hardware requirements=</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=2. Hardware requirements=</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Because of the nature of the data being processed, it is better if your computer has at least 200 MB of free RAM per thread (>1GB per thread for large databases). Nonetheless, it is possible to run CrocoBLAST on large files even if less memory is available, but you will need to manually specify a small fragment size during job submission. Furthermore, if you need to analyze NGS data,the input and output files involved in such calculations can be quite large, and therefore you will need to have sufficient space on your hard disk. NCBI databases range from 10 MB to 500 GB (whole genomes). Depending on the type of sequencing experiment you ran, your input files may range from a few kB to hundreds of GB. If you don't specify any BLAST options, the size of the output file may be up to 1500 times the size of the input file. Nevertheless, in the typical use case, requesting relevant BLAST options (e.g., provide only the first 20 hits) will greatly reduce the size of the output file.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Because of the nature of the data being processed, it is better if your computer has at least 200 MB of free RAM per thread (>1GB per thread for large databases). Nonetheless, it is possible to run CrocoBLAST on large files even if less memory is available, but you will need to manually specify a small fragment size during job submission. Furthermore, if you need to analyze NGS data,the input and output files involved in such calculations can be quite large, and therefore you will need to have sufficient space on your hard disk. NCBI databases range from 10 MB to 500 GB (whole genomes). Depending on the type of sequencing experiment you ran, your input files may range from a few kB to hundreds of GB. If you don't specify any BLAST options, the size of the output file may be up to 1500 times the size of the input file. Nevertheless, in the typical use case, requesting relevant BLAST options (e.g., provide only the first 20 hits) will greatly reduce the size of the output file.</div></td></tr> </table>

Crina