Mercurial > repos > fubar > htseq_bams_to_count_matrix

changeset 3:77b192678083 draft

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Uploaded
author fubar
date Thu, 06 Jun 2013 20:20:25 -0400
parents 4800361923a0
children 7a3dcdc81ddd
files htseq_bams_to_count_matrix/htseqsams2mx.xml htseq_bams_to_count_matrix/tool_dependencies.xml htseq_bams_to_count_matrix/tool_dependencies.xml.notworkingcomplex
diffstat 3 files changed, 30 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/htseq_bams_to_count_matrix/htseqsams2mx.xml	Thu Jun 06 08:37:30 2013 -0400
+++ b/htseq_bams_to_count_matrix/htseqsams2mx.xml	Thu Jun 06 20:20:25 2013 -0400
@@ -2,6 +2,8 @@
     <description>for DGE</description>
     <requirements>
       <requirement type="package" version="0.5.4">package_htseq_0_5_4</requirement>
+      <requirement type="package" version="0.5.4">package_numpy_1_7</requirement>
+      <requirement type="package" version="0.5.4">package_matplotlib_1_2</requirement>
     </requirements>
     <command interpreter="python">
     htseqsams2mx.py -g "$gfffile" -o "$outfile" -m "$model" --id_attribute "$id_attr" --feature_type "$feature_type"
--- a/htseq_bams_to_count_matrix/tool_dependencies.xml	Thu Jun 06 08:37:30 2013 -0400
+++ b/htseq_bams_to_count_matrix/tool_dependencies.xml	Thu Jun 06 20:20:25 2013 -0400
@@ -1,6 +1,26 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="package_htseq_0_5_4" version="0.5.4">
-       <repository name="package_htseq_0_5_4" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu" changeset_revision="7574983a942a"/>
+    <package name="package_htseq_0_5_4" version="0.5.4p3">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p3.tar.gz</action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
+                <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
+                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Numpy Python package.
+        </readme>
+    </package>
+    <package name="package_numpy_1_7" version="1.7.1">
+        <repository changeset_revision="af9633757cf0" name="package_numpy_1_7" owner="blankenberg" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="package_matplotlib_1_2" version="1.2">
+        <repository changeset_revision="c888aa8ed318" name="package_matplotlib_1_2" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/htseq_bams_to_count_matrix/tool_dependencies.xml.notworkingcomplex	Thu Jun 06 20:20:25 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="package_htseq_0_5_4" version="0.5.4">
+       <repository name="package_htseq_0_5_4" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu" changeset_revision="7574983a942a"/>
+    </package>
+</tool_dependency>