# HG changeset patch
# User lparsons
# Date 1383600258 18000
# Node ID 65c91537862c99c484076fb4ed1266670ccb8585
# Parent  1615d0b5b809fcc0a59fe0d952836d00b4755f38
Updated to HTSeq 0.5.4p5, use tool shed repository dependencies

diff -r 1615d0b5b809 -r 65c91537862c .hgignore
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.hgignore	Mon Nov 04 16:24:18 2013 -0500
@@ -0,0 +1,3 @@
+^package$
+syntax: glob
+*.pyc
diff -r 1615d0b5b809 -r 65c91537862c .hgtags
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.hgtags	Mon Nov 04 16:24:18 2013 -0500
@@ -0,0 +1,3 @@
+142ec9462fa644cd29642ea0ad10e9889ce75619 0.3
+3e7b1e8a69f9d79b8de603f24e466deb7b192100 0.3.release2
+496a7dc0786f8367264520dfff6e8e8e744de3b2 0.3.1
diff -r 1615d0b5b809 -r 65c91537862c fabfile.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fabfile.py	Mon Nov 04 16:24:18 2013 -0500
@@ -0,0 +1,26 @@
+from fabric.api import local
+from fabric.operations import prompt
+import os
+
+
+def package():
+    '''
+    Pacakge for upload to toolshed
+      packaging 'test' version (default) uses local directory
+      otherwise, specify a mercurial tag to package
+    '''
+    package_dir = 'package'
+    base_filename = os.path.join(package_dir, 'htseq-count')
+    version = prompt("Enter version number for package [test]:")
+    revision_option = ''
+    if version != '':
+        revision_option = '-r "%s"' % version
+    else:
+        version = 'test'
+    version_filename = '%s_%s.tar.gz' % (base_filename, version)
+    local('mkdir -p %s' % package_dir)
+    local('rm -f %s' % version_filename)
+    if version == 'test':
+        local('tar czvf %s --exclude "fabfile.*" --exclude "%s" --exclude ".hg*" *' % (version_filename, package_dir))
+    else:
+        local('hg archive -t tgz %s -X "fabfile.*" -X "package" -X ".hg*" -p . "%s"' % (revision_option, version_filename))
diff -r 1615d0b5b809 -r 65c91537862c htseq-count.xml
--- a/htseq-count.xml	Fri Mar 22 13:40:24 2013 -0400
+++ b/htseq-count.xml	Mon Nov 04 16:24:18 2013 -0500
@@ -1,10 +1,10 @@
-<tool id="htseq_count" name="htseq-count" version="0.3.1">
+<tool id="htseq_count" name="htseq-count" version="0.3.2">
     <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="package" version="1.6.2">numpy</requirement>
-        <requirement type="package" version="0.5.4p1">htseq</requirement>
-        <requirement type="package" version="0.1.18">samtools</requirement>
+        <requirement type="package" version="1.7.1">numpy</requirement>
+        <requirement type="package" version="0.5.4p5">htseq</requirement>
+        <requirement type="package" version="0.1.19">samtools</requirement>
         <requirement type="package" version="1.56.0">picard</requirement> 
     </requirements>
     <command>
@@ -188,7 +188,7 @@
 
 The following figure illustrates the effect of these three modes:
 
-.. image:: ./static/images/count_modes.png
+.. image:: $PATH_TO_IMAGES/count_modes.png
     :width: 500
 
 
diff -r 1615d0b5b809 -r 65c91537862c test-data/._htseq-test-paired_counts.tsv
Binary file test-data/._htseq-test-paired_counts.tsv has changed
diff -r 1615d0b5b809 -r 65c91537862c test-data/._htseq-test-paired_othercounts.tsv
Binary file test-data/._htseq-test-paired_othercounts.tsv has changed
diff -r 1615d0b5b809 -r 65c91537862c tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Mar 22 13:40:24 2013 -0400
+++ b/tool_dependencies.xml	Mon Nov 04 16:24:18 2013 -0500
@@ -1,31 +1,28 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="numpy" version="1.6.2">
+
+    <package name="numpy" version="1.7.1">
+        <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="samtools" version="1.1.19">
+        <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="picard" version="1.56.0">
+        <repository changeset_revision="7206dbf34dcd" name="package_picard_1_56_0" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="htseq" version="0.5.4p5">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.tar.gz</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 --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
-                <action type="set_environment">
-                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
-
-    <package name="htseq" version="0.5.4p1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p1.tar.gz</action>
+                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p5.tar.gz</action>
                 <action type="make_directory">$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 $INSTALL_DIR/bin</action>
                 <action type="set_environment">
-                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <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>
@@ -34,44 +31,4 @@
         </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">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            Compiling SAMtools requires the ncurses and zlib development libraries.
-        </readme>
-    </package>
-
-    <package name="picard" version="1.56.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action>
-                <action type="move_directory_files">
-                    <source_directory>picard-tools-1.56</source_directory>
-                    <destination_directory>$INSTALL_DIR/jars</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
 </tool_dependency>