Mercurial > repos > vimalkumarvelayudhan > riboplot
changeset 26:4b1254319802
Attempt 3 using virtualenv
| author | Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> |
|---|---|
| date | Tue, 01 Sep 2015 17:50:38 +0100 |
| parents | 80d8e91e8b46 |
| children | 99dda3e39997 |
| files | ribocount.xml riboplot.xml tool_dependencies.xml |
| diffstat | 3 files changed, 7 insertions(+), 2 deletions(-) [+] |
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--- a/ribocount.xml Tue Sep 01 17:12:59 2015 +0100 +++ b/ribocount.xml Tue Sep 01 17:50:38 2015 +0100 @@ -7,7 +7,7 @@ <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> - <command>ribocount + <command interpreter="python">${RIBOPLOT_PATH}/ribocount --ribo_file "${ribo_file}" --transcriptome_fasta "${transcriptome_fasta}" --read_length "${read_length}"
--- a/riboplot.xml Tue Sep 01 17:12:59 2015 +0100 +++ b/riboplot.xml Tue Sep 01 17:50:38 2015 +0100 @@ -7,7 +7,7 @@ <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> - <command>riboplot + <command interpreter="python">${RIBOPLOT_PATH}/riboplot --ribo_file "${ribo_file}" --transcriptome_fasta "${transcriptome_fasta}" --transcript_name "${transcript_name}"
--- a/tool_dependencies.xml Tue Sep 01 17:12:59 2015 +0100 +++ b/tool_dependencies.xml Tue Sep 01 17:50:38 2015 +0100 @@ -4,6 +4,11 @@ <install version="1.0"> <actions> <action type="setup_virtualenv">riboplot==0.1.0</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="set_to" name="RIBOPLOT_PATH">$INSTALL_DIR/bin</environment_variable> + </action> </actions> </install> <readme>