Mercurial > repos > yhoogstrate > package_crossmap_0_2

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
author yhoogstrate
date Wed, 26 Aug 2015 11:03:59 -0400
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children 803db5577b07
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-1:000000000000 0:805c8fbd3b4e
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="numpy" version="1.9">
4 <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6
7 <package name="cython" version="0.20.1">
8 <repository changeset_revision="c3a8c46fcb97" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
9 </package>
10
11 <package name="crossmap" version="0.2">
12 <install version="1.0">
13 <actions>
14 <action sha256sum="eb983c8d0ff0331f069e2378768d8988b6b9d8dd303a0f0f0cef9d882256af85" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.tar.gz</action>
15
16 <action type="setup_python_environment">
17 <repository changeset_revision="c3a8c46fcb97" name="package_cython_0_20_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
18 <package name="cython" version="0.20.1" />
19 </repository>
20 <repository changeset_revision="d6f39c80e75b" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
21 <package name="numpy" version="1.9" />
22 </repository>
23 </action>
24
25 <!-- CrossMap doesn't pick up the correct Cython path.
26 Therefore install it with a manual shell_command instead
27 of <package></package> inside a pyton_env. -->
28 <action type="shell_command">
29 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1(sig_list)/" "bin/CrossMap.py" ;
30
31 export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &amp;&amp;
32
33 python setup.py install --root $INSTALL_DIR
34 </action>
35
36 <action type="set_environment">
37 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/site-packages</environment_variable>
38 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/dist-packages</environment_variable>
39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable>
40
41 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/usr/local/bin</environment_variable>
42 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
43 </action>
44 </actions>
45 </install>
46 <readme>
47 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
48 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
49 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
50 and VCF, reading from remote servers and file compression are supported.
51
52 NEWS:
53 * 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.
54 * 07/27/15: Release version 0.1.9. For VCF file conversion in v0.1.9:
55 - CrossMap uses the indexed reference genome (target assembly) sequences rather than load
56 the entire file into memory. Users could index their reference genome file using samtools faidx
57 before running CrossMap, otherwise CrossMap will index it automatically the first time you run it.
58 - In the output VCF file, whether the chromosome IDs contain "chr" or not depends on the input
59 format.
60 * 05/15/15: Release version 0.1.8: Fixed the bug that CrossMap will output invalid VCF file when the
61 input VCF file contains a INFO field with whitespace.
62 * 05/04/15: Release version 0.1.7: Address the problem that CrossMap does not convert strand in
63 inversions when input file is BED6 or BED12 format.
64 * 11/06/14: Release version 0.1.6: Fixed "negative coordinates" bug.
65 * 08/05/14: Release version 0.1.5: Support compressed (*.gz, *.Z, *.z, *.bz, *.bz2, *.bzip2) wiggle file
66 as input.
67 * 05/19/14: add chain files for hg38-&gt;hg19, hg19-&gt;hg38, hg18-&gt;hg38, hg19-&gt;GRCh37,
68 GRCh37-&gt;hg19. In CrossMap v0.1.4, conversion results of BAM/SAM files can be directed to
69 STDOUT to support piping.
70 * 12/12/13: CrossMap was accepted by Bioinformatics
71 * 10/23/13: CrossMap (0.1.3) was released
72
73 Documentation: http://crossmap.sourceforge.net/
74 </readme>
75 </package>
76 </tool_dependency>