Mercurial > repos > lparsons > htseq_count

changeset 2:8f0f896ec527

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Added tool_dependencies.xml
author Lance Parsons <lparsons@princeton.edu>
date Fri, 31 Aug 2012 15:23:53 -0400
parents 4de3f044aaeb
children c6d73933f601
files htseq-count.xml tool_dependencies.xml
diffstat 2 files changed, 56 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/htseq-count.xml	Fri Aug 31 14:54:56 2012 -0400
+++ b/htseq-count.xml	Fri Aug 31 15:23:53 2012 -0400
@@ -2,7 +2,8 @@
     <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
     <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command>
     <requirements>
-        <requirement type="python-package" version="0.5.3.p9">HTSeq</requirement>
+        <requirement type="package" version="1.6.2">numpy</requirement>
+        <requirement type="package" version="0.5.3.p9">htseq</requirement>
         <requirement type="package" version="0.1.18">samtools</requirement>
     </requirements>
     <command>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Aug 31 15:23:53 2012 -0400
@@ -0,0 +1,54 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="numpy" version="1.6.2">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/numpy/NumPy/1.6.2/numpy-1.6.2.tar.gz</action>
+                <action type="shell_command">python setup.py install --home $INSTALL_DIR</action>
+                <action type="set_environment">
+                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
+                </action>
+            </actions>
+        </install>
+    </package>
+    <package name="htseq" version="0.5.3p9">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action>
+                <action type="set_environment">
+                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
+                </action>
+                <action type="shell_command">python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            HTSeq requires that Numpy be installed.
+        </readme>
+    </package>
+    <package name="samtools" version="0.1.18">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
+                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>samtools</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>misc/maq2sam-long</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Compiling SAMtools requires the ncurses and zlib development libraries.
+        </readme>
+    </package>
+</tool_dependency>