Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv14161
Added Files:
bowtie2.info bowtie2.patch
Log Message:
new package bowtie2
--- NEW FILE: bowtie2.info ---
Package: bowtie2
Version: 2.1.0
Revision: 1
Description: Ultrafast memory-efficient short read aligner
License: GPL
Maintainer: Hanspeter Niederstrasser <[email protected]>
BuildDepends: help2man
Source: mirror:sourceforge:bowtie-bio/%n-%v-source.zip
Source-MD5: 1d10f079d6dd560320f0309bd70f6080
SourceDirectory: %n-%v
PatchFile: %n.patch
PatchFile-MD5: 28f8721894039a307f516acb9b9ba3b4
CompileScript: <<
make
<<
InstallScript: <<
#!/bin/sh -ev
make install PREFIX=%p DESTDIR=%d
<<
DocFiles: AUTHORS LICENSE MANUAL MANUAL.markdown NEWS TUTORIAL VERSION
Homepage: http://bowtie-bio.sourceforge.net/
DescDetail: <<
An ultrafast and memory-efficient tool for aligning sequencing reads
to long reference sequences. It is particularly good at aligning reads
of about 50 up to 100s or 1,000s of characters, and particularly good
at aligning to relatively long (e.g. mammalian) genomes.
Bowtie 2 indexes the genome with an FM Index to keep its memory footprint
small: for the human genome, its memory footprint is typically
around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
<<
DescPackaging: <<
Made new install targets to generate man pages (via Ubuntu example)
and to help install things.
<<
--- NEW FILE: bowtie2.patch ---
diff -ruN bowtie2-2.1.0-orig/Makefile bowtie2-2.1.0/Makefile
--- bowtie2-2.1.0-orig/Makefile 2013-02-18 16:00:49.000000000 -0500
+++ bowtie2-2.1.0/Makefile 2013-03-11 10:24:08.000000000 -0400
@@ -329,3 +329,26 @@
bowtie2-src.zip bowtie2-bin.zip
rm -f core.* .tmp.head
rm -rf *.dSYM
+
+.PHONY: man
+man:
+ help2man --name="wrapper for bowtie2-align" --no-info \
+ `pwd`/bowtie2 > bowtie2.1
+ help2man --name="building a colorspace index for bowtie2" --no-info \
+ `pwd`/bowtie2-build > bowtie2-build.1
+ help2man --name="extracts information from a bowtie2 index" --no-info \
+ `pwd`/bowtie2-inspect > bowtie2-inspect.1
+ help2man --name="ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences" --no-info \
+ `pwd`/bowtie2-align> bowtie2-align.1
+
+.PHONY: install
+install: all doc man
+ mkdir -p $(DESTDIR)$(PREFIX)/bin
+ cp $(BOWTIE2_BIN_LIST) $(DESTDIR)$(PREFIX)/bin
+ mkdir -p $(DESTDIR)$(PREFIX)/share/doc/bowtie2
+ cp -R doc/* $(DESTDIR)$(PREFIX)/share/doc/bowtie2
+ mkdir -p $(DESTDIR)$(PREFIX)/share/man/man1
+ cp bowtie2{,-build,-inspect,-align}.1 $(DESTDIR)$(PREFIX)/share/man/man1
+ mkdir -p $(DESTDIR)$(PREFIX)/share/bowtie2/examples
+ cp -R example/* $(DESTDIR)$(PREFIX)/share/bowtie2/examples
+ cp -R scripts $(DESTDIR)$(PREFIX)/share/bowtie2/examples
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