Mercurial > repos > yhoogstrate > featurecounts
changeset 7:2312bedfe2a3 draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Wed, 19 Nov 2014 10:07:59 -0500 |
| parents | fae19d64e9de |
| children | 1a288d568ac1 |
| files | README.md README.rst featurecounts.xml tool_dependencies.xml |
| diffstat | 4 files changed, 64 insertions(+), 71 deletions(-) [+] |
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--- a/README.md Thu Nov 13 09:46:22 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ -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/>.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed Nov 19 10:07:59 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 Thu Nov 13 09:46:22 2014 -0500 +++ b/featurecounts.xml Wed Nov 19 10:07:59 2014 -0500 @@ -236,7 +236,7 @@ License ------- -featureCounts / subread package: +**featureCounts / subread package**: - GNU General Public License version 3.0 (GPLv3) @@ -246,12 +246,16 @@ 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 toolsheds: -- http://toolshed.dtls.nl/ -- http://toolshed.g2.bx.psu.edu -- http://testtoolshed.g2.bx.psu.edu/ + +http://toolshed.dtls.nl/ + +http://toolshed.g2.bx.psu.edu/ + +http://testtoolshed.g2.bx.psu.edu/ </help> </tool>
--- a/tool_dependencies.xml Thu Nov 13 09:46:22 2014 -0500 +++ b/tool_dependencies.xml Wed Nov 19 10:07:59 2014 -0500 @@ -22,24 +22,13 @@ <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="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/featurecounts2bed.sh $INSTALL_DIR/bin/</action> <action type="chmod"> - <file mode="555">$INSTALL_DIR/bin/featurecounts2bed.sh</file> + <file mode="755">$INSTALL_DIR/bin/featurecounts2bed.sh</file> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> </action> </actions> </install>