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author yhoogstrate
date Tue, 04 Aug 2015 08:15:49 -0400
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45 CrossMap is versatile tool to convert genome coordinates or annotation files between genome 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, 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 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. 48 and VCF, reading from remote servers and file compression are supported.
49 49
50 Installation 50 NEWS:
51 51 * 05/15/15: Release version 0.1.8: Fixed the bug that CrossMap will output invalid VCF file when the
52 Prerequisite: 52 input VCF file contains a INFO field with whitespace.
53 * gcc 53 * 05/04/15: Release version 0.1.7: Address the problem that CrossMap does not convert strand in
54 * python2.7 or newer 54 inversions when input file is BED6 or BED12 format.
55 * numpy 55 * 11/06/14: Release version 0.1.6: Fixed "negative coordinates" bug.
56 * cython 56 * 08/05/14: Release version 0.1.5: Support compressed (*.gz, *.Z, *.z, *.bz, *.bz2, *.bzip2) wiggle file
57 57 as input.
58 Download CrossMap program from here: 58 * 05/19/14: add chain files for hg38->hg19, hg19->hg38, hg18->hg38, hg19->GRCh37,
59 59 GRCh37->hg19. In CrossMap v0.1.4, conversion results of BAM/SAM files can be directed to
60 $ tar zxf CrossMap-VERSION.tar.gz 60 STDOUT to support piping.
61 61 * 12/12/13: CrossMap was accepted by Bioinformatics
62 $ cd CrossMap-VERSION 62 * 10/23/13: CrossMap (0.1.3) was released
63
64 # install CrossMap to default location. In Linux/Unix, this location is like:
65 # /home/user/lib/python2.7/site-packages/
66 $ python setup.py install
67
68 # or you can install CrossMap to a specified location:
69 $ python setup.py install --root=/home/user/CrossMap
70
71 # setup PYTHONPATH. Skip this step if CrossMap was installed to default location.
72 $ export PYTHONPATH=/home/user/CrossMap/usr/local/lib/python2.7/site-packages:$PYTHONPATH.
73
74 # Skip this step if CrossMap was installed to default location.
75 $ export PATH=/home/user/CrossMap/usr/local/bin:$PATH
76
77 NOTE:
78
79 * Due to intensive computation, CrossMap is designed to run on Linux/Unix and Mac OS. Some modules may not work properly on Windows.
80 * Mac users need to download and install Xcode command line tools.
81 63
82 Documentation: http://crossmap.sourceforge.net/ 64 Documentation: http://crossmap.sourceforge.net/
83 </readme> 65 </readme>
84 </package> 66 </package>
85 </tool_dependency> 67 </tool_dependency>