changeset 0:805c8fbd3b4e draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Aug 26 11:03:59 2015 -0400
@@ -0,0 +1,76 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    
+    <package name="cython" version="0.20.1">
+        <repository changeset_revision="c3a8c46fcb97" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    
+    <package name="crossmap" version="0.2">
+        <install version="1.0">
+            <actions>
+                <action sha256sum="eb983c8d0ff0331f069e2378768d8988b6b9d8dd303a0f0f0cef9d882256af85" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.tar.gz</action>
+                
+                <action type="setup_python_environment">
+                    <repository changeset_revision="c3a8c46fcb97" name="package_cython_0_20_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="cython" version="0.20.1" />
+                    </repository>
+                    <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.9" />
+                    </repository>
+                </action>
+                
+                <!-- CrossMap doesn't pick up the correct Cython path.
+                Therefore install it with a manual shell_command instead
+                of <package></package> inside a pyton_env. -->
+                <action type="shell_command">
+                    sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1(sig_list)/" "bin/CrossMap.py" ;
+                    
+                    export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &amp;&amp;
+                    
+                    python setup.py install --root $INSTALL_DIR
+                </action>
+                
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/site-packages</environment_variable>
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/dist-packages</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable>
+                    
+                    <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/usr/local/bin</environment_variable>
+                    <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+CrossMap is versatile tool to convert genome coordinates or annotation files between genome
+assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
+GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
+and VCF, reading from remote servers and file compression are supported.
+
+NEWS:
+ * 08/11/15: Release version 0.2: Fixed the bug that CrossMap will not convert wiggle format files due to name collision with bx python.
+ * 07/27/15: Release version 0.1.9. For VCF file conversion in v0.1.9:
+  - CrossMap uses the indexed reference genome (target assembly) sequences rather than load
+the entire file into memory. Users could index their reference genome file using samtools faidx
+before running CrossMap, otherwise CrossMap will index it automatically the first time you run it.
+  - In the output VCF file, whether the chromosome IDs contain "chr" or not depends on the input
+format.
+ * 05/15/15: Release version 0.1.8: Fixed the bug that CrossMap will output invalid VCF file when the
+input VCF file contains a INFO field with whitespace.
+ * 05/04/15: Release version 0.1.7: Address the problem that CrossMap does not convert strand in
+inversions when input file is BED6 or BED12 format.
+ * 11/06/14: Release version 0.1.6: Fixed "negative coordinates" bug.
+ * 08/05/14: Release version 0.1.5: Support compressed (*.gz, *.Z, *.z, *.bz, *.bz2, *.bzip2) wiggle file
+as input.
+ * 05/19/14: add chain files for hg38-&gt;hg19, hg19-&gt;hg38, hg18-&gt;hg38, hg19-&gt;GRCh37,
+GRCh37-&gt;hg19. In CrossMap v0.1.4, conversion results of BAM/SAM files can be directed to
+STDOUT to support piping.
+ * 12/12/13: CrossMap was accepted by Bioinformatics
+ * 10/23/13: CrossMap (0.1.3) was released
+ 
+Documentation: http://crossmap.sourceforge.net/
+        </readme>
+    </package>
+</tool_dependency>