Mercurial > repos > yhoogstrate > featurecounts
changeset 6:fae19d64e9de draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Thu, 13 Nov 2014 09:46:22 -0500 |
| parents | 31279ea9fbfa |
| children | 2312bedfe2a3 |
| files | README.md featurecounts.xml featurecounts2bed.sh tool_dependencies.xml |
| diffstat | 4 files changed, 95 insertions(+), 13 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Thu Nov 13 09:46:22 2014 -0500 @@ -0,0 +1,53 @@ +FeatureCounts wrapper for Galaxy +================================ + +<http://bioinf.wehi.edu.au/featureCounts/> +<http://subread.sourceforge.net/> + +FeatureCounts as part of the SUBREAD package is "a highly efficient and +accurate read summarization program". + +Development +----------- + +* Repository-Maintainer: Youri Hoogstrate + +* Repository-Development: <https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools> + +The tool wrapper has been written by Youri Hoogstrate from the Erasmus +Medical Center (Rotterdam, Netherlands) on behalf of the Translational +Research IT (TraIT) project: + +<http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch> + +More tools by the Translational Research IT (TraIT) project can be found in the following repository: + +<http://toolshed.dtls.nl/> + +License +------- + +**featureCounts**: + +GPL (>=3) + +**featurecounts2bed**: + +GPL (>=3) + +**This wrapper**: + + Copyright (C) 2013-2014 Youri Hoogstrate + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>.
--- a/featurecounts.xml Wed May 21 08:27:05 2014 -0400 +++ b/featurecounts.xml Thu Nov 13 09:46:22 2014 -0500 @@ -1,10 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="featurecounts" name="featureCounts"> +<tool id="featurecounts" name="featureCounts" version="1.4.4.a"> <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description> <requirements> <requirement type="package" version="1.4.4">featurecounts</requirement> <requirement type="package" version="1.0.0">featurecounts2bed</requirement> </requirements> + <version_command>featureCounts -v</version_command> <command> <!-- The following script is written in the "Cheetah" language: @@ -226,7 +227,7 @@ **featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.** -*Liao Y1, Smyth GK, Shi W.* Bioinformatics. 2014 Apr 1;30(7):923-30. +*Liao Y1, Smyth GK, Shi W.* - Bioinformatics. 2014 Apr 1;30(7):923-30. - http://www.ncbi.nlm.nih.gov/pubmed/24227677 - http://dx.doi.org/10.1093/bioinformatics/btt656 @@ -242,13 +243,15 @@ Contact ------- -The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project: +The tool wrapper has been written by Youri Hoogstrate from the Erasmus +Medical Center (Rotterdam, Netherlands) on behalf of the Translational +Research IT (TraIT) project: http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch -I want to thank the Marius van den Beek for his contribution to this wrapper. - -More tools by the Translational Research IT (TraIT) project can be found in the following repository: -http://testtoolshed.g2.bx.psu.edu/ - +More tools by the Translational Research IT (TraIT) project can be found +in the following toolsheds: +- http://toolshed.dtls.nl/ +- http://toolshed.g2.bx.psu.edu +- http://testtoolshed.g2.bx.psu.edu/ </help> -</tool> \ No newline at end of file +</tool>
--- a/featurecounts2bed.sh Wed May 21 08:27:05 2014 -0400 +++ b/featurecounts2bed.sh Thu Nov 13 09:46:22 2014 -0500 @@ -1,5 +1,20 @@ #!/bin/bash +# featurecounts2bed - converts featureCounts output to BED format + +# Copyright 2013-2014, Youri Hoogstrate + +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License at <http://www.gnu.org/licenses/> for +# more details. + # This tool has been written by Youri Hoogstrate from the Erasmus # Medical Center (Rotterdam, Netherlands) on behalf of the Translational # Research IT (TraIT) project: @@ -9,6 +24,7 @@ # found in the following repository: # http://toolshed.dtls.nl/ + exon_level="true" filename=""
--- a/tool_dependencies.xml Wed May 21 08:27:05 2014 -0400 +++ b/tool_dependencies.xml Thu Nov 13 09:46:22 2014 -0500 @@ -6,30 +6,40 @@ <action type="shell_command">wget http://sourceforge.net/projects/subread/files/subread-1.4.4/subread-1.4.4-source.tar.gz && tar -zxvf subread-1.4.4-source.tar.gz && cd subread-1.4.4-source/src/ && make -f Makefile.Linux && cd ../../</action> <action type="move_file"> <source>../subread-1.4.4-source/bin/featureCounts</source> - <destination>$INSTALL_DIR/bin</destination> + <destination>$INSTALL_DIR/bin/</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> + <!--<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>--> </action> </actions> </install> <readme> - Downloads and installs featureCounts; requires WGET, GNU AUTOTOOLS and TAR to be installed! + Downloads and installs featureCounts; requires WGET, GNU AUTOTOOLS and TAR to be installed. </readme> </package> <package name="featurecounts2bed" version="1.0.0"> <install version="1.0"> <actions> + <action type="move_file"> + <source>$REPOSITORY_INSTALL_DIR/featurecounts2bed.sh</source> + <destination>$INSTALL_DIR/bin/</destination> + </action> + <!-- + Revert to the previous if the move command doesn't work + <action type="shell_command">wget http://testtoolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/raw-file/tip/featurecounts2bed.sh && chmod 755 *.sh</action> <action type="move_file"> <source>../featurecounts2bed.sh</source> <destination>$INSTALL_DIR/bin</destination> </action> + --> + <action type="chmod"> + <file mode="555">$INSTALL_DIR/bin/featurecounts2bed.sh</file> + </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> </action> </actions> </install>