Mercurial > repos > vimalkumarvelayudhan > riboplot
changeset 27:99dda3e39997
Attempt 4 using virtualenv
| author | Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> |
|---|---|
| date | Wed, 02 Sep 2015 12:23:20 +0100 |
| parents | 4b1254319802 |
| children | 60bbd8ebe314 |
| files | ribocount.xml riboplot.xml tool_dependencies.xml |
| diffstat | 3 files changed, 3 insertions(+), 5 deletions(-) [+] |
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--- a/ribocount.xml Tue Sep 01 17:50:38 2015 +0100 +++ b/ribocount.xml Wed Sep 02 12:23:20 2015 +0100 @@ -7,7 +7,7 @@ <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> - <command interpreter="python">${RIBOPLOT_PATH}/ribocount + <command>python \${RIBOPLOT_PATH}/ribocount --ribo_file "${ribo_file}" --transcriptome_fasta "${transcriptome_fasta}" --read_length "${read_length}"
--- a/riboplot.xml Tue Sep 01 17:50:38 2015 +0100 +++ b/riboplot.xml Wed Sep 02 12:23:20 2015 +0100 @@ -7,7 +7,7 @@ <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> - <command interpreter="python">${RIBOPLOT_PATH}/riboplot + <command>python \${RIBOPLOT_PATH}/riboplot --ribo_file "${ribo_file}" --transcriptome_fasta "${transcriptome_fasta}" --transcript_name "${transcript_name}"
--- a/tool_dependencies.xml Tue Sep 01 17:50:38 2015 +0100 +++ b/tool_dependencies.xml Wed Sep 02 12:23:20 2015 +0100 @@ -5,9 +5,7 @@ <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">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="set_to" name="RIBOPLOT_PATH">$INSTALL_DIR/venv/bin</environment_variable> </action> </actions> </install>