| Previous changeset 2:d2283cca00cd (2016-10-18) Next changeset 4:cd6a48ffd093 (2018-09-26) |
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Commit message:
Version 1.0.2-3: move to conda-based dependency resolution. |
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modified:
README.rst ceas_wrapper.xml data_manager/data_manager_ceas_fetch_annotations.xml test-data/ceas_out1.log.re_match test-data/ceas_out2.log.re_match test-data/ceas_out3.log.re_match |
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removed:
tool_dependencies.xml |
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| diff -r d2283cca00cd -r df54f8fcc7a7 README.rst --- a/README.rst Tue Oct 18 09:31:10 2016 -0400 +++ b/README.rst Wed Feb 28 10:22:32 2018 -0500 |
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| @@ -67,8 +67,7 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- -1.0.2-3 - Switch to getting R 3.1.2 and bx-python 0.7.1 dependencies from the - toolshed (rather than installing as part of the tool) +1.0.2-3 - Updated to fetch all dependencies from conda 1.0.2-2 - Major updates to fix various bugs, add tests and enable ceasBW to be used without an existing chromosome sizes file. 1.0.2-1 - Modified to work with Cistrome-version of CEAS (includes additional |
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| diff -r d2283cca00cd -r df54f8fcc7a7 ceas_wrapper.xml --- a/ceas_wrapper.xml Tue Oct 18 09:31:10 2016 -0400 +++ b/ceas_wrapper.xml Wed Feb 28 10:22:32 2018 -0500 |
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| @@ -1,14 +1,12 @@ <tool id="ceas" name="CEAS" version="1.0.2-3"> <description>Annotate intervals and scores with genome features</description> <requirements> - <requirement type="package" version="1.2.5">python_mysqldb</requirement> - <requirement type="package" version="0.7.1">bx-python</requirement> - <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement> - <requirement type="package" version="1.0">ucsc_fetchChromSizes</requirement> - <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="1.0.2b1">cistrome-ceas</requirement> + <requirement type="package" version="357">ucsc-fetchchromsizes</requirement> </requirements> <version_command>ceas --version 2>&1 | tail -1</version_command> - <command interpreter="bash">ceas_wrapper.sh + <command><![CDATA[ + bash $__tool_directory__/ceas_wrapper.sh $bed_file ${gdb_file.fields.path} $log_output $pdf_report $xls_output #if (str($wig_file) != 'None') @@ -28,7 +26,8 @@ --sizes $sizes_lower,$sizes_middle,$sizes_upper --bisizes $bisizes_lower,$bisizes_upper --pf-res $profiling_resolution - --rel-dist $relative_distance</command> + --rel-dist $relative_distance + ]]></command> <inputs> <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" /> <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true" |
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| diff -r d2283cca00cd -r df54f8fcc7a7 data_manager/data_manager_ceas_fetch_annotations.xml --- a/data_manager/data_manager_ceas_fetch_annotations.xml Tue Oct 18 09:31:10 2016 -0400 +++ b/data_manager/data_manager_ceas_fetch_annotations.xml Wed Feb 28 10:22:32 2018 -0500 |
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| @@ -1,8 +1,6 @@ <tool id="data_manager_fetch_ceas_annotations" name="Fetch CEAS annotation" version="0.0.1" tool_type="manage_data"> <requirements> - <requirement type="package" version="1.2.5">python_mysqldb</requirement> - <requirement type="package" version="0.7.1">bx_python</requirement> - <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement> + <requirement type="package" version="1.0.2b1">cistrome-ceas</requirement> </requirements> <description>Fetch and install annotation databases for CEAS</description> <command interpreter="python">data_manager_ceas_fetch_annotations.py |
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| diff -r d2283cca00cd -r df54f8fcc7a7 test-data/ceas_out1.log.re_match --- a/test-data/ceas_out1.log.re_match Tue Oct 18 09:31:10 2016 -0400 +++ b/test-data/ceas_out1.log.re_match Wed Feb 28 10:22:32 2018 -0500 |
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| @@ -23,8 +23,8 @@ INFO\ \ \@\ .*\ \#6\ perform\ ChIP\ region\ annotation\.\.\.\ INFO\ \ \@\ .*\ \#7\ write\ a\ R\ script\ of\ ChIP\ region\ annotation\.\.\.\ -R\ version\ 3\.1\.2\ \(2014\-10\-31\)\ \-\-\ \"Pumpkin\ Helmet\" -Copyright\ \(C\)\ 2014\ The\ R\ Foundation\ for\ Statistical\ Computing +R\ version\ .* +Copyright\ \(C\)\ 20(\d\d)\ The\ R\ Foundation\ for\ Statistical\ Computing Platform\:\ .* R\ is\ free\ software\ and\ comes\ with\ ABSOLUTELY\ NO\ WARRANTY\. |
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| diff -r d2283cca00cd -r df54f8fcc7a7 test-data/ceas_out2.log.re_match --- a/test-data/ceas_out2.log.re_match Tue Oct 18 09:31:10 2016 -0400 +++ b/test-data/ceas_out2.log.re_match Wed Feb 28 10:22:32 2018 -0500 |
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| @@ -27,8 +27,8 @@ INFO\ \ \@\ .*\ \#8\-1\ run\ wig\ profiling\ of\ chr26\.\.\.\ INFO\ \ \@\ .*\ \#9\ append\ an\ R\ script\ of\ wig\ profiling\.\.\.\ -R\ version\ 3\.1\.2\ \(2014\-10\-31\)\ \-\-\ \"Pumpkin\ Helmet\" -Copyright\ \(C\)\ 2014\ The\ R\ Foundation\ for\ Statistical\ Computing +R\ version\ .* +Copyright\ \(C\)\ 20(\d\d)\ The\ R\ Foundation\ for\ Statistical\ Computing Platform\:\ .* R\ is\ free\ software\ and\ comes\ with\ ABSOLUTELY\ NO\ WARRANTY\. |
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| diff -r d2283cca00cd -r df54f8fcc7a7 test-data/ceas_out3.log.re_match --- a/test-data/ceas_out3.log.re_match Tue Oct 18 09:31:10 2016 -0400 +++ b/test-data/ceas_out3.log.re_match Wed Feb 28 10:22:32 2018 -0500 |
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| @@ -27,8 +27,8 @@ INFO\ \ \@\ .*\ \#8\-1\ run\ wig\ profiling\ of\ chr26\.\.\.\ INFO\ \ \@\ .*\ \#9\ append\ an\ R\ script\ of\ wig\ profiling\.\.\.\ -R\ version\ 3\.1\.2\ \(2014\-10\-31\)\ \-\-\ \"Pumpkin\ Helmet\" -Copyright\ \(C\)\ 2014\ The\ R\ Foundation\ for\ Statistical\ Computing +R\ version\ .* +Copyright\ \(C\)\ 20(\d\d)\ The\ R\ Foundation\ for\ Statistical\ Computing Platform\:\ .* R\ is\ free\ software\ and\ comes\ with\ ABSOLUTELY\ NO\ WARRANTY\. |
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| diff -r d2283cca00cd -r df54f8fcc7a7 tool_dependencies.xml --- a/tool_dependencies.xml Tue Oct 18 09:31:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,87 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <!-- R 3.1.2 from main/test toolshed --> - <package name="R" version="3.1.2"> - <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <!-- bx_python from main/test toolshed --> - <package name="bx-python" version="0.7.1"> - <repository changeset_revision="7ce9cf37130f" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <!-- Python mysqldb package --> - <package name="python_mysqldb" version="1.2.5"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://pypi.python.org/packages/source/M/MySQL-python/MySQL-python-1.2.5.zip</action> - <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="shell_command"> - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && - python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme>Installs Python module MySQLdb 1.2.5</readme> - </package> - <!-- cistrome_ceas - Installs the version of CEAS package found in the Cistrome - distribution: - https://bitbucket.org/cistrome/cistrome-applications-harvard/overview - --> - <package name="cistrome_ceas" version="1.0.2.d8c0751"> - <install version="1.0"> - <actions> - <action type="shell_command"> - hg clone https://bitbucket.org/cistrome/cistrome-applications-harvard cistrome_ceas - </action> - <action type="shell_command"> - hg update d8c0751 - </action> - <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="shell_command"> - cd published-packages/CEAS/ - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && - python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme>Installs version 1.0.2 of CEAS from cistrome (commit id d8c0751, - datestamp 20140929), which includes ceasBW (a version of ceas which can - handle bigWig file input from MACS2. - - Cistrome code is at - https://bitbucket.org/cistrome/cistrome-applications-harvard/overview - - The CEAS code is under the published-packages/CEAS/ subdirectory - - Cistrome data files and documentation can be found at - http://liulab.dfci.harvard.edu/CEAS/index.html - </readme> - </package> - <!-- fetchChromSize from UCSC tools --> - <package name="ucsc_fetchChromSizes" version="1.0"> - <install version="1.0"> - <actions> - <action type="download_binary"> - <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template> - </action> - <action type="chmod"> - <file mode="755">$INSTALL_DIR/fetchChromSizes</file> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme>Installs the binary executable for the fetchChromSizes utility - from UCSC tools - </readme> - </package> -</tool_dependency> |