Michał T. Lorenc mictadlo
mictadlo
/ docker-compose-output
Created
March 19, 2018 12:44
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| ``` | |
| Attaching to mgsvdocker_db_1, mgsvdocker_www_1 | |
| www_1 | AH00558: apache2: Could not reliably determine the server's fully qualified domain name, using 172.20.0.3. Set the 'ServerName' directive globally to suppress this message | |
| www_1 | AH00558: apache2: Could not reliably determine the server's fully qualified domain name, using 172.20.0.3. Set the 'ServerName' directive globally to suppress this message | |
| www_1 | [Mon Mar 19 12:37:49.657134 2018] [mpm_prefork:notice] [pid 1] AH00163: Apache/2.4.10 (Debian) PHP/5.6.34 configured -- resuming normal operations | |
| www_1 | [Mon Mar 19 12:37:49.671610 2018] [core:notice] [pid 1] AH00094: Command line: 'apache2 -D FOREGROUND' | |
| db_1 | 2018-03-19T12:37:49.783928Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details). | |
| db_1 | 2018-03-19T12:37:49.785163Z 0 [Note] mysqld (mysqld 5.7.21) starting as process 1 ... | |
| db_1 | 2018-03-19T12:37:49.791836Z 0 [Note] Inn |
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| # Howto | |
| cd samtools | |
| docker build -t samtools . | |
| cd ../samtools-run | |
| docker build -t samtools-run . | |
| docker run -it -e LOCAL_USER_ID=`id -u $USER` samtools-run | |
| user@d2a1d8faa190:/usr/local/samtools-0.1.19$ samtools |
mictadlo
/ easybuild-Boost-1.51.0-20161003.225253.sSoQq.log
Created
October 3, 2016 23:27
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| == 2016-10-03 22:52:53,320 easyblock.py:254 INFO This is EasyBuild 2.9.0 (framework: 2.9.0, easyblocks: 2.9.0) on host waterhouse-1. | |
| == 2016-10-03 22:52:53,321 easyblock.py:260 INFO This is easyblock EB_Boost from module easybuild.easyblocks.boost (/mnt/easybuild/software/EasyBuild/2.9.0/lib/python2.7/site-packages/easybuild_easyblocks-2.9.0-py2.7.egg/easybuild/easyblocks/b/boost.pyo) | |
| == 2016-10-03 22:52:53,321 easyblock.py:746 INFO Build dir set to /mnt/easybuild/build/Boost/1.51.0/goolf-1.4.10 | |
| == 2016-10-03 22:52:53,321 easyblock.py:785 INFO Software install dir set to /mnt/easybuild/software/Boost/1.51.0-goolf-1.4.10 | |
| == 2016-10-03 22:52:53,322 easyblock.py:790 INFO Module install dir set to /mnt/easybuild/modules/all | |
| == 2016-10-03 22:52:53,322 easyblock.py:239 INFO Init completed for application name Boost version 1.51.0 | |
| == 2016-10-03 22:52:53,322 easyblock.py:2354 INFO Obtained application instance of for Boost (easyblock: None) | |
| == 2016-10-03 22:52:53,322 build_log.py:238 INFO building and installing Boos |
mictadlo
/ easybuild-Boost-1.51.0-20161003.225253.sSoQq.log
Created
October 3, 2016 23:27
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| == 2016-10-03 22:52:53,320 easyblock.py:254 INFO This is EasyBuild 2.9.0 (framework: 2.9.0, easyblocks: 2.9.0) on host waterhouse-1. | |
| == 2016-10-03 22:52:53,321 easyblock.py:260 INFO This is easyblock EB_Boost from module easybuild.easyblocks.boost (/mnt/easybuild/software/EasyBuild/2.9.0/lib/python2.7/site-packages/easybuild_easyblocks-2.9.0-py2.7.egg/easybuild/easyblocks/b/boost.pyo) | |
| == 2016-10-03 22:52:53,321 easyblock.py:746 INFO Build dir set to /mnt/easybuild/build/Boost/1.51.0/goolf-1.4.10 | |
| == 2016-10-03 22:52:53,321 easyblock.py:785 INFO Software install dir set to /mnt/easybuild/software/Boost/1.51.0-goolf-1.4.10 | |
| == 2016-10-03 22:52:53,322 easyblock.py:790 INFO Module install dir set to /mnt/easybuild/modules/all | |
| == 2016-10-03 22:52:53,322 easyblock.py:239 INFO Init completed for application name Boost version 1.51.0 | |
| == 2016-10-03 22:52:53,322 easyblock.py:2354 INFO Obtained application instance of for Boost (easyblock: None) | |
| == 2016-10-03 22:52:53,322 build_log.py:238 INFO building and installing Boos |
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| #Chip-Seq | |
| # These tools returned many hits | |
| * ssp | |
| * Macs | |
| * homer | |
| * meme | |
| # I could not find a Galaxy for this one: |
mictadlo
/ Test output
Created
August 3, 2015 23:54
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| /Users/lorencm/.virtualenvs/galaxy/bin/python /Users/lorencm/projects/galaxy/importTools2Galaxy.py | |
| 1 snpEff | |
| OrderedDict([(u'@file', u'toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a/galaxy/snpSift_filter.xml'), (u'@guid', u'toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpSift_filter/1.0'), (u'tool_shed', u'toolshed.g2.bx.psu.edu'), (u'repository_name', u'snpeff'), (u'repository_owner', u'pcingola'), (u'installed_changeset_revision', u'c052639fa666'), (u'id', u'toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpSift_filter/1.0'), (u'version', u'1.0')]) | |
| OrderedDict([(u'@file', u'toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a/galaxy/snpEff.xml'), (u'@guid', u'toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpEff/1.0'), (u'tool_shed', u'toolshed.g2.bx.psu.edu'), (u'repository_name', u'snpeff'), (u'repository_owner', u'pcingola'), (u'installed_changeset_revision', u'c052639fa666'), (u'id', u'toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/s |
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| Traceback (most recent call last): | |
| File "importTools2Galaxy.py", line 12, in <module> | |
| tool_section_name = section['@name'] | |
| TypeError: string indices must be integers |
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| <html><head> | |
| <meta charset="utf-8"> | |
| <title>SnpEff example</title> | |
| </head> | |
| <body> | |
| <a name="effects"> | |
| <center> | |
| <b> Number of effects by type and region </b> <p> | |
| <table border="0"> |