| Previous changeset 6:85214e4428fd (2015-09-11) Next changeset 8:d79fe626c6fd (2015-10-22) |
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Commit message:
v0.1.7.0 bug fixes |
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modified:
cloudmap.xml tool_dependencies.xml |
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| diff -r 85214e4428fd -r 3619e85a5477 cloudmap.xml --- a/cloudmap.xml Fri Sep 11 16:25:49 2015 +0200 +++ b/cloudmap.xml Tue Sep 22 22:36:41 2015 +0200 |
| b |
| @@ -1,12 +1,9 @@ <tool id="nacreousmap" name="NacreousMap" version="0.1.7.0"> <description>Map causative mutations by multi-variant linkage analysis.</description> - <macros> - <import>toolshed_macros.xml</import> - </macros> <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> - mimodd map "${opt.source.ifile}" ${opt.mode} + mimodd map ${opt.mode} "${opt.source.ifile}" #if $str($opt.source.sample): -m "${opt.source.sample}" #end if @@ -60,6 +57,7 @@ </command> <macros> + <import>toolshed_macros.xml</import> <macro name="svd_unconditional"> <expand macro="hidden_vaf_algo_params" /> <expand macro="seqdict_param" /> @@ -122,7 +120,7 @@ <param name="infer_missing" type="hidden" value="" /> </macro> <macro name="bins"> - <repeat name="bin_sizes" title="bin sizes to analyze variants in (defaults to: 1Mb and 500Kb" default="0" min="0" help="Values can be entered in bases (e.g., 1000000), kilobases (e.g., 500Kb) or megabases (e.g., 1Mb), but must be integral, i.e. no decimal numbers are allowed."> + <repeat name="bin_sizes" title="bin sizes to analyze variants in (defaults to: 1Mb and 500Kb)" default="0" min="0" help="Values can be entered in bases (e.g., 1000000), kilobases (e.g., 500Kb) or megabases (e.g., 1Mb), but must be integral, i.e. no decimal numbers are allowed."> <param name="bin_size" type="text" /> </repeat> </macro> |
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| diff -r 85214e4428fd -r 3619e85a5477 tool_dependencies.xml --- a/tool_dependencies.xml Fri Sep 11 16:25:49 2015 +0200 +++ b/tool_dependencies.xml Tue Sep 22 22:36:41 2015 +0200 |
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| @@ -29,8 +29,9 @@ <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action> <!-- make MiModD's wrapped binaries executable --> <action type="shell_command">chmod 755 $INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</action> - - + <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself --> + <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action> + <action type="set_environment"> <!-- make the mimodd entry script discoverable --> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable> |