Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv25372
Added Files:
samtools.info tabix.info vcftools.info vcftools.patch
Log Message:
new packages for next generation sequencing analysis
--- NEW FILE: vcftools.info ---
Package: vcftools
Version: 0.1.10
Revision: 1
Description: Tools for VCF files
License: GPL
Maintainer: Hanspeter Niederstrasser <[email protected]>
Source: mirror:sourceforge:%n/%n_%v.tar.gz
Source-MD5: c21f0d1be99e98571ef6422da4765f2a
PatchFile: %n.patch
PatchFile-MD5: 7150c38873d6facd46b034a22938a27c
#PatchScript: <<
# %{default_script}
#<<
CompileScript: <<
make CPP=clang++ PREFIX=%p
<<
#InfoTest: <<
# TestScript: <<
# PERL5LIB=%b/perl:$PERL5LIB PATH=%b/perl:$PATH perl/test.t ||
exit 2
# <<
# TestDepends: <<
# tabix,
# test-most-pm5123
# <<
#<<
InstallScript: <<
#!/bin/sh -ev
make install PREFIX=%p DESTDIR=%d
mkdir -p %i/share/%n/examples
cp -p examples/* %i/share/%n/examples
chmod 755 %i/bin/*
<<
DocFiles: README.txt
Homepage: http://vcftools.sourceforge.net/
DescDetail: <<
Program package designed for working with VCF files, such as
those generated by the 1000 Genomes Project. The aim of VCFtools
is to provide methods for working with VCF files: validating,
merging, comparing and calculate some basic population genetic
statistics.
<<
DescPackaging: <<
Patched Makefiles because they did not understand a packaging workflow
into a temporary install directory.
Internal perlmods go into %p/lib/perl5, not %p/lib/perl5/site_perl
<<
--- NEW FILE: vcftools.patch ---
diff -ruN vcftools_0.1.10-orig/Makefile vcftools_0.1.10/Makefile
--- vcftools_0.1.10-orig/Makefile 2012-12-04 03:27:43.000000000 -0500
+++ vcftools_0.1.10/Makefile 2013-01-14 10:58:09.000000000 -0500
@@ -17,12 +17,17 @@
export PREFIX = $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
endif
export BINDIR = ${PREFIX}/bin
-export MODDIR = ${PREFIX}/lib/perl5/site_perl
+export MODDIR = ${PREFIX}/lib/perl5
+export DESTDIR =
DIRS = cpp perl
+
+vcftools:
+ for dir in $(DIRS); do cd $$dir && $(MAKE) && cd ..; done
+
install:
- @mkdir -p $(BINDIR); mkdir -p $(MODDIR); \
- for dir in $(DIRS); do cd $$dir && $(MAKE) $(MAKEFLAGS) && cd ..; done
+ mkdir -p $(DESTDIR)$(BINDIR); mkdir -p $(DESTDIR)$(MODDIR);
+ for dir in $(DIRS); do cd $$dir && $(MAKE) install && cd ..; done
clean:
@for dir in $(DIRS); do cd $$dir && $(MAKE) clean && cd ..; done
diff -ruN vcftools_0.1.10-orig/cpp/Makefile vcftools_0.1.10/cpp/Makefile
--- vcftools_0.1.10-orig/cpp/Makefile 2012-12-04 03:27:39.000000000 -0500
+++ vcftools_0.1.10/cpp/Makefile 2013-01-14 10:46:35.000000000 -0500
@@ -36,8 +36,10 @@
vcftools: $(OBJS)
$(CPP) $(OBJS) -o vcftools $(LIB)
+
+install:
ifdef BINDIR
- cp $(CURDIR)/$@ $(BINDIR)/$@
+ cp $(CURDIR)/vcftools $(DESTDIR)$(BINDIR)/vcftools
endif
# pull in dependency info for *existing* .o files
diff -ruN vcftools_0.1.10-orig/perl/Makefile vcftools_0.1.10/perl/Makefile
--- vcftools_0.1.10-orig/perl/Makefile 2012-12-04 03:27:41.000000000 -0500
+++ vcftools_0.1.10/perl/Makefile 2013-01-14 10:45:40.000000000 -0500
@@ -1,12 +1,14 @@
-BIN = fill-aa fill-an-ac fill-fs fill-ref-md5 fill-rsIDs vcf-annotate
vcf-compare vcf-concat \
- vcf-consensus vcf-contrast vcf-convert vcf-filter vcf-fix-ploidy
vcf-indel-stats vcf-isec vcf-merge vcf-phased-join \
+BIN = fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare
vcf-concat \
+ vcf-consensus vcf-contrast vcf-convert vcf-fix-ploidy vcf-indel-stats
vcf-isec vcf-merge vcf-phased-join \
vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab
vcf-tstv vcf-validator
MOD = FaSlice.pm Vcf.pm VcfStats.pm
+vcftools:
+
install:
- @for i in $(BIN); do cp $(CURDIR)/$$i $(BINDIR)/$$i; done; \
- for i in $(MOD); do cp $(CURDIR)/$$i $(MODDIR)/$$i; done;
+ @for i in $(BIN); do cp $(CURDIR)/$$i $(DESTDIR)$(BINDIR)/$$i;
done; \
+ for i in $(MOD); do cp $(CURDIR)/$$i $(DESTDIR)$(MODDIR)/$$i; done;
clean:
@for i in $(BIN); do rm -f $(BINDIR)/$$i; done; \
--- NEW FILE: tabix.info ---
Package: tabix
Version: 0.2.6
Revision: 1
Description: Indexer for TAB-delimited genome files
License: BSD
Maintainer: Hanspeter Niederstrasser <[email protected]>
Depends: <<
<<
BuildDepends: <<
<<
Source: mirror:sourceforge:samtools/%n-%v.tar.bz2
Source-MD5: 36a61ceac2f5bed36018434282bbcc5d
CompileScript: <<
make
<<
InstallScript: <<
#!/bin/sh -ev
mkdir -p %i/bin
install -m 0755 tabix %i/bin
mkdir -p %i/share/man/man1
install -m 0644 tabix.1 %i/share/man/man1
mkdir -p %i/share/%n/examples
install -m 0644 example.gtf.gz* %i/share/%n/examples
<<
DocFiles: ChangeLog NEWS tabix.tex
Homepage: http://samtools.sourceforge.net/
DescDetail: <<
Tabix indexes a TAB-delimited genome position file in.tab.bgz and
creates an index file in.tab.bgz.tbi when region is absent from the
command-line. The input data file must be position sorted and
compressed by bgzip which has a gzip(1) like interface. After
indexing, tabix is able to quickly retrieve data lines overlapping
regions specified in the format "chr:beginPos-endPos". Fast data
retrieval also works over network if URI is given as a file name
and in this case the index file will be downloaded if it is not
present locally.
<<
--- NEW FILE: samtools.info ---
Package: samtools
Version: 0.1.18
Revision: 1
Description: Tools for SAM alignment files
License: BSD
Maintainer: Hanspeter Niederstrasser <[email protected]>
Depends: <<
<<
BuildDepends: <<
<<
Source: mirror:sourceforge:%n/%v/%n-%v.tar.bz2
Source-MD5: 71dab132e21c0766f0de84c2371a9157
PatchScript: <<
### clang doesn't like inline void
perl -pi -e 's|inline void __ks_insertsort_|static inline void
__ks_insertsort_|g' ksort.h
<<
CompileScript: <<
make -w
make -w razip bgzip
make -C bcftools bcftools
<<
InstallScript: <<
#!/bin/sh -ev
mkdir -p %i/bin
install -m 0755 bgzip razip samtools %i/bin
install -m 0755 bcftools/{bcftools,vcfutils.pl} %i/bin
install -m 0755
misc/{blast2sam.pl,bowtie2sam.pl,export2sam.pl,maq2sam-long,maq2sam-short,md5fa,md5sum-lite,novo2sam.pl,psl2sam.pl,sam2vcf.pl,samtools.pl,seqtk,soap2sam.pl,varfilter.py,wgsim,wgsim_eval.pl,zoom2sam.pl}
%i/bin
mkdir -p %i/share/man/man1
install -m 0644 samtools.1 %i/share/man/man1
<<
DocFiles: AUTHORS COPYING ChangeLog NEWS bcftools/README:README.bfctools
Homepage: http://samtools.sourceforge.net/
DescDetail: <<
SAM Tools provide various utilities for manipulating alignments in
the SAM format, including sorting, merging, indexing and generating
alignments in a per-position format.
<<
DescUsage: <<
<<
DescPackaging: <<
<<
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_jan
_______________________________________________
Fink-commits mailing list
[email protected]
http://news.gmane.org/gmane.os.apple.fink.cvs
