Mercurial > repos > lparsons > htseq_count

changeset 13:30bb8acb77a4

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Updated to v0.5.4p5, use repository dependencies.
author lparsons
date Tue, 05 Nov 2013 13:02:43 -0500
parents 62a1de8c8aae
children 265ca0f35789
files .hgignore .hgtags README.md fabfile.py htseq-count.xml tool_dependencies.xml
diffstat 6 files changed, 110 insertions(+), 64 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.hgignore	Tue Nov 05 13:02:43 2013 -0500
@@ -0,0 +1,3 @@
+^package$
+syntax: glob
+*.pyc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.hgtags	Tue Nov 05 13:02:43 2013 -0500
@@ -0,0 +1,3 @@
+142ec9462fa644cd29642ea0ad10e9889ce75619 0.3
+3e7b1e8a69f9d79b8de603f24e466deb7b192100 0.3.release2
+496a7dc0786f8367264520dfff6e8e8e744de3b2 0.3.1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Tue Nov 05 13:02:43 2013 -0500
@@ -0,0 +1,51 @@
+htseq-count wrapper for Galaxy
+==============================
+
+Galaxy wrapper for
+[htseq-count](http://www-huber.embl.de/users/anders/HTSeq/doc/count.html)
+script from python
+[HTSeq](http://www-huber.embl.de/users/anders/HTSeq/doc/index.html) package.
+
+Installation
+------------
+
+Installtion directly from the [Galaxy
+Toolshed](http://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count) is
+recommended.
+
+Development
+-----------
+
+Repository-Maintainer: Lance Parsons <lparsons@princeton.edu>
+
+Repository-Development: <https://bitbucket.org/lance_parsons/htseq_count_galaxy_wrapper>
+
+
+License
+-------
+
+Copyright (c) 2012-2013, Lance R. Parsons <lparsons@princeton.edu>  
+All rights reserved.
+
+Licensed under the BSD 2-Clause License: <http://opensource.org/licenses/BSD-2-Clause>
+    
+    Redistribution and use in source and binary forms, with or without
+    modification, are permitted provided that the following conditions are met:
+    
+        * Redistributions of source code must retain the above copyright notice,
+          this list of conditions and the following disclaimer.
+    
+        * Redistributions in binary form must reproduce the above copyright notice,
+          this list of conditions and the following disclaimer in the documentation
+          and/or other materials provided with the distribution.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+    ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+    WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+    FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+    DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+    SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+    CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+    OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fabfile.py	Tue Nov 05 13:02:43 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))
--- a/htseq-count.xml	Mon Mar 11 12:44:45 2013 -0400
+++ b/htseq-count.xml	Tue Nov 05 13:02:43 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
 
 
--- a/tool_dependencies.xml	Mon Mar 11 12:44:45 2013 -0400
+++ b/tool_dependencies.xml	Tue Nov 05 13:02:43 2013 -0500
@@ -1,31 +1,34 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="numpy" version="1.6.2">
+
+    <package name="numpy" version="1.7.1">
+        <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="picard" version="1.56.0">
+        <repository changeset_revision="61e41d21cb6f" name="package_picard_1_56_0" owner="devteam" toolshed="http://toolshed.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">$INSTALL_DIR/bin</environment_variable>
+                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p5.tar.gz</action>
+                <!-- populate the environment variables from the dependend repos -->
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.7.1" />
+                   </repository>
                 </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
-
-    <package name="htseq" version="0.5.4p1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p1.tar.gz</action>
                 <action type="make_directory">$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 +37,4 @@
         </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>