Mercurial > repos > pjbriggs > ceas
changeset 2:d2283cca00cd draft
CEAS tool version 1.0.2-3: updates to get R 3.1.2 and bx-python 0.7.1 dependencies from the toolshed.
| author | pjbriggs |
|---|---|
| date | Tue, 18 Oct 2016 09:31:10 -0400 |
| parents | df9033b88b53 |
| children | df54f8fcc7a7 |
| files | README.rst ceas_wrapper.xml tool_dependencies.xml |
| diffstat | 3 files changed, 10 insertions(+), 35 deletions(-) [+] |
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--- a/README.rst Thu Aug 11 04:16:49 2016 -0400 +++ b/README.rst Tue Oct 18 09:31:10 2016 -0400 @@ -67,6 +67,8 @@ ========== ====================================================================== 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) 1.0.2-2 - 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
--- a/ceas_wrapper.xml Thu Aug 11 04:16:49 2016 -0400 +++ b/ceas_wrapper.xml Tue Oct 18 09:31:10 2016 -0400 @@ -1,8 +1,8 @@ -<tool id="ceas" name="CEAS" version="1.0.2-2"> +<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="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>
--- a/tool_dependencies.xml Thu Aug 11 04:16:49 2016 -0400 +++ b/tool_dependencies.xml Tue Oct 18 09:31:10 2016 -0400 @@ -1,17 +1,12 @@ <?xml version="1.0"?> <tool_dependency> - <!-- Local version of R 3.1.2 dependency --> + <!-- R 3.1.2 from main/test toolshed --> <package name="R" version="3.1.2"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.2.tar.gz</action> - <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> - <action type="make_install" /> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> + <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"> @@ -31,28 +26,6 @@ </install> <readme>Installs Python module MySQLdb 1.2.5</readme> </package> - <!-- bx_python - This is cribbed from devteam's 'package_bx_python_0_7' in the main - toolshed: - https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7 - --> - <package name="bx_python" version="0.7.1"> - <install version="1.0"> - <actions> - <action type="setup_virtualenv"> -numpy==1.7.1 -bx-python==0.7.1 - </action> - <action type="set_environment"> - <environment_variable action="set_to" name="BX_PYTHON_PATH">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme> - Installation of bx-python 0.7.1 along with numpy 1.7.1. The installation can be - accessed via BX_PYTHON_PATH. - </readme> - </package> <!-- cistrome_ceas Installs the version of CEAS package found in the Cistrome distribution: