| Previous changeset 26:4b1254319802 (2015-09-01) Next changeset 28:60bbd8ebe314 (2015-09-02) |
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Commit message:
Attempt 4 using virtualenv |
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modified:
ribocount.xml riboplot.xml tool_dependencies.xml |
| b |
| diff -r 4b1254319802 -r 99dda3e39997 ribocount.xml --- a/ribocount.xml Tue Sep 01 17:50:38 2015 +0100 +++ b/ribocount.xml Wed Sep 02 12:23:20 2015 +0100 |
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| @@ -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}" |
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| diff -r 4b1254319802 -r 99dda3e39997 riboplot.xml --- a/riboplot.xml Tue Sep 01 17:50:38 2015 +0100 +++ b/riboplot.xml Wed Sep 02 12:23:20 2015 +0100 |
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| @@ -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}" |
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| diff -r 4b1254319802 -r 99dda3e39997 tool_dependencies.xml --- a/tool_dependencies.xml Tue Sep 01 17:50:38 2015 +0100 +++ b/tool_dependencies.xml Wed Sep 02 12:23:20 2015 +0100 |
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| @@ -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> |