Mercurial > repos > yhoogstrate > package_crossmap_0_1_8

changeset 14:467e88009c12 draft default tip

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Uploaded
author yhoogstrate
date Tue, 04 Aug 2015 08:15:49 -0400
parents ebe9034b7450
children
files tool_dependencies.xml
diffstat 1 files changed, 13 insertions(+), 31 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Jul 22 08:29:09 2015 -0400
+++ b/tool_dependencies.xml	Tue Aug 04 08:15:49 2015 -0400
@@ -47,37 +47,19 @@
 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.
 
-Installation
-
-Prerequisite:
- * gcc
- * python2.7 or newer
- * numpy
- * cython
-
-Download CrossMap program from here:
-
-$ tar zxf CrossMap-VERSION.tar.gz
-
-$ cd CrossMap-VERSION
-
-# install CrossMap to default location. In Linux/Unix, this location is like:
-# /home/user/lib/python2.7/site-packages/
-$ python setup.py install
-
-# or you can install CrossMap to a specified location:
-$ python setup.py install --root=/home/user/CrossMap
-
-# setup PYTHONPATH. Skip this step if CrossMap was installed to default location.
-$ export PYTHONPATH=/home/user/CrossMap/usr/local/lib/python2.7/site-packages:$PYTHONPATH.
-
-# Skip this step if CrossMap was installed to default location.
-$ export PATH=/home/user/CrossMap/usr/local/bin:$PATH
-
-NOTE:
-
- * Due to intensive computation, CrossMap is designed to run on Linux/Unix and Mac OS. Some modules may not work properly on Windows.
- * Mac users need to download and install Xcode command line tools.
+NEWS:
+ * 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->hg19, hg19->hg38, hg18->hg38, hg19->GRCh37,
+GRCh37->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>