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Michał T. Lorenc mictadlo

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View docker-compose-output
```
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
@mictadlo
mictadlo / Howto
Created Oct 21, 2016
command not found inside Docker
View Howto
# 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
View easybuild-Boost-1.51.0-20161003.225253.sSoQq.log
This file has been truncated, but you can view the full file.
== 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)
View easybuild-Boost-1.51.0-20161003.225253.sSoQq.log
This file has been truncated, but you can view the full file.
== 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)
View chip-seq
#Chip-Seq
# These tools returned many hits
* ssp
* Macs
* homer
* meme
# I could not find a Galaxy for this one:
View Test output
/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
@mictadlo
mictadlo / error.out
Created Aug 3, 2015
TypeError: string indices must be integers with XMLtoDict
View error.out
Traceback (most recent call last):
File "importTools2Galaxy.py", line 12, in <module>
tool_section_name = section['@name']
TypeError: string indices must be integers
@mictadlo
mictadlo / SnpEff.html
Last active Aug 29, 2015
Little snpEff example
View SnpEff.html
<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">
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