Mercurial > repos > pjbriggs > ceas

changeset 3:df54f8fcc7a7 draft

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Version 1.0.2-3: move to conda-based dependency resolution.
author pjbriggs
date Wed, 28 Feb 2018 10:22:32 -0500
parents d2283cca00cd
children cd6a48ffd093
files 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 tool_dependencies.xml
diffstat 7 files changed, 14 insertions(+), 105 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Tue Oct 18 09:31:10 2016 -0400
+++ b/README.rst	Wed Feb 28 10:22:32 2018 -0500
@@ -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
--- a/ceas_wrapper.xml	Tue Oct 18 09:31:10 2016 -0400
+++ b/ceas_wrapper.xml	Wed Feb 28 10:22:32 2018 -0500
@@ -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&gt;&amp;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"
--- 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
@@ -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
--- 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
@@ -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\.
--- 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
@@ -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\.
--- 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
@@ -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\.
--- a/tool_dependencies.xml	Tue Oct 18 09:31:10 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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 &amp;&amp; 
-          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 &amp;&amp; 
-          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>