|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
|
3 <package name="numpy" version="1.9">
|
|
11
|
4 <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
|
|
0
|
5 </package>
|
|
|
6
|
|
|
7 <package name="cython" version="0.20.1">
|
|
|
8 <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
|
|
|
9 </package>
|
|
|
10
|
|
|
11 <package name="crossmap" version="0.1.8">
|
|
|
12 <install version="1.0">
|
|
|
13 <actions>
|
|
13
|
14 <action sha256sum="c4586d8ac2b2cc3910eea07b6f65b5d62d335b741ad91afb63f14cde22b3706f" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.1.8.tar.gz</action>
|
|
8
|
15
|
|
0
|
16 <action type="setup_python_environment">
|
|
6
|
17 <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
|
|
|
18 <package name="cython" version="0.20.1" />
|
|
0
|
19 </repository>
|
|
11
|
20 <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
|
|
6
|
21 <package name="numpy" version="1.9" />
|
|
0
|
22 </repository>
|
|
8
|
23 </action>
|
|
|
24
|
|
9
|
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 the pyton_env. -->
|
|
8
|
28 <action type="shell_command">
|
|
|
29 export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &&
|
|
9
|
30
|
|
12
|
31 python setup.py install --root $INSTALL_DIR
|
|
0
|
32 </action>
|
|
3
|
33
|
|
0
|
34 <action type="set_environment">
|
|
|
35 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/site-packages</environment_variable>
|
|
13
|
36 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/dist-packages</environment_variable>
|
|
0
|
37 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable>
|
|
|
38
|
|
|
39 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/usr/local/bin</environment_variable>
|
|
|
40 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
|
|
|
41 </action>
|
|
|
42 </actions>
|
|
|
43 </install>
|
|
|
44 <readme>
|
|
|
45 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
|
|
|
46 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
|
|
|
47 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
|
|
|
48 and VCF, reading from remote servers and file compression are supported.
|
|
|
49
|
|
14
|
50 NEWS:
|
|
|
51 * 05/15/15: Release version 0.1.8: Fixed the bug that CrossMap will output invalid VCF file when the
|
|
|
52 input VCF file contains a INFO field with whitespace.
|
|
|
53 * 05/04/15: Release version 0.1.7: Address the problem that CrossMap does not convert strand in
|
|
|
54 inversions when input file is BED6 or BED12 format.
|
|
|
55 * 11/06/14: Release version 0.1.6: Fixed "negative coordinates" bug.
|
|
|
56 * 08/05/14: Release version 0.1.5: Support compressed (*.gz, *.Z, *.z, *.bz, *.bz2, *.bzip2) wiggle file
|
|
|
57 as input.
|
|
|
58 * 05/19/14: add chain files for hg38->hg19, hg19->hg38, hg18->hg38, hg19->GRCh37,
|
|
|
59 GRCh37->hg19. In CrossMap v0.1.4, conversion results of BAM/SAM files can be directed to
|
|
|
60 STDOUT to support piping.
|
|
|
61 * 12/12/13: CrossMap was accepted by Bioinformatics
|
|
|
62 * 10/23/13: CrossMap (0.1.3) was released
|
|
0
|
63
|
|
|
64 Documentation: http://crossmap.sourceforge.net/
|
|
|
65 </readme>
|
|
|
66 </package>
|
|
|
67 </tool_dependency>
|
