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| author | Renato Alves <alves.rjc@gmail.com> | 2018-02-02 02:51:34 +0100 |
|---|---|---|
| committer | Renato Alves <alves.rjc@gmail.com> | 2018-02-02 21:49:50 +0100 |
| commit | 65ea5f8857654d6edcb796fbadd42e39f832b666 (patch) | |
| tree | f14645d736cc4d9c81912d2d94937cf67d95bc17 /pkgs/applications | |
| parent | 43f647e5b44a875a7928790a6a5628af1f9350c5 (diff) | |
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samtools_0_1_19: init at 0.1.19
samtools-1.5 already exists but some software requires the older version
Diffstat (limited to 'pkgs/applications')
| -rw-r--r-- | pkgs/applications/science/biology/samtools/samtools-0.1.19-no-curses.patch | 22 | ||||
| -rw-r--r-- | pkgs/applications/science/biology/samtools/samtools_0_1_19.nix | 34 |
2 files changed, 56 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/samtools/samtools-0.1.19-no-curses.patch b/pkgs/applications/science/biology/samtools/samtools-0.1.19-no-curses.patch new file mode 100644 index 00000000000..a7782a1a026 --- /dev/null +++ b/pkgs/applications/science/biology/samtools/samtools-0.1.19-no-curses.patch @@ -0,0 +1,22 @@ +diff --git a/Makefile b/Makefile +index 2f51bfc..395d6f1 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,7 +1,7 @@ + CC= gcc + CFLAGS= -g -Wall -O2 + #LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib +-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 ++DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE # -D_CURSES_LIB=1 + KNETFILE_O= knetfile.o + LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ + bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \ +@@ -15,7 +15,7 @@ PROG= samtools + INCLUDES= -I. + SUBDIRS= . bcftools misc + LIBPATH= +-LIBCURSES= -lcurses # -lXCurses ++LIBCURSES= # -lcurses # -lXCurses + + .SUFFIXES:.c .o + .PHONY: all lib diff --git a/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix b/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix new file mode 100644 index 00000000000..a811bc4412f --- /dev/null +++ b/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix @@ -0,0 +1,34 @@ +{ stdenv, fetchurl, zlib }: + +stdenv.mkDerivation rec { + name = "${pname}-${version}"; + pname = "samtools"; + version = "0.1.19"; + + src = fetchurl { + url = "mirror://sourceforge/samtools/${name}.tar.bz2"; + sha256 = "d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4"; + }; + + patches = [ + ./samtools-0.1.19-no-curses.patch + ]; + + buildInputs = [ zlib ]; + + installPhase = '' + mkdir -p $out/bin + mkdir -p $out/share/man + + cp samtools $out/bin + cp samtools.1 $out/share/man + ''; + + meta = with stdenv.lib; { + description = "Tools for manipulating SAM/BAM/CRAM format"; + license = licenses.mit; + homepage = http://samtools.sourceforge.net/; + platforms = platforms.unix; + maintainers = [ maintainers.unode ]; + }; +} |