diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 43 | ||||
| -rw-r--r-- | gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch | 37 | ||||
| -rw-r--r-- | gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch | 33 |
3 files changed, 18 insertions, 95 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4ae1ad0470..35cec1edfb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2590,46 +2590,39 @@ structures, classes for genomic regions, mapped sequencing reads, etc.") (define-public preseq (package (name "preseq") - (version "1.0.2") + (version "2.0") (source (origin (method url-fetch) - (uri - (string-append "http://smithlabresearch.org/downloads/preseq-" - version ".tar.bz2")) + (uri (string-append "https://github.com/smithlabcode/" + "preseq/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc")) - (patches (list (search-patch "preseq-1.0.2-install-to-PREFIX.patch") - (search-patch "preseq-1.0.2-link-with-libbam.patch"))) + (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq")) (modules '((guix build utils))) (snippet ;; Remove bundled samtools. - '(delete-file-recursively "preseq-master/samtools")))) + '(delete-file-recursively "samtools")))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target #:phases (modify-phases %standard-phases - (add-after - 'unpack 'enter-dir - (lambda _ - (chdir "preseq-master") - #t)) - (add-after - 'enter-dir 'use-samtools-headers - (lambda _ - (substitute* '("smithlab_cpp/SAM.cpp" - "smithlab_cpp/SAM.hpp") - (("sam.h") "samtools/sam.h")) - #t)) (delete 'configure)) - #:make-flags (list (string-append "PREFIX=" - (assoc-ref %outputs "out")) - (string-append "LIBBAM=" - (assoc-ref %build-inputs "samtools") - "/lib/libbam.a")))) + #:make-flags + (list (string-append "PREFIX=" + (assoc-ref %outputs "out")) + (string-append "LIBBAM=" + (assoc-ref %build-inputs "samtools") + "/lib/libbam.a") + (string-append "SMITHLAB_CPP=" + (assoc-ref %build-inputs "smithlab-cpp") + "/lib") + "PROGS=preseq" + "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)"))) (inputs `(("gsl" ,gsl) ("samtools" ,samtools-0.1) + ("smithlab-cpp" ,smithlab-cpp) ("zlib" ,zlib))) (home-page "http://smithlabresearch.org/software/preseq/") (synopsis "Program for analyzing library complexity") diff --git a/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch b/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch deleted file mode 100644 index f8318ae0f5..0000000000 --- a/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch +++ /dev/null @@ -1,37 +0,0 @@ -This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15 - -From 65387b0d766e6c06a15cf8d8f9183d9a4ba644bb Mon Sep 17 00:00:00 2001 -From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> -Date: Thu, 25 Jun 2015 15:01:53 +0200 -Subject: [PATCH] Install to PREFIX - ---- - Makefile | 8 ++++++-- - 1 file changed, 6 insertions(+), 2 deletions(-) - -diff --git a/Makefile b/Makefile -index 4d0367a..e334f2f 100644 ---- a/preseq-master/Makefile -+++ b/preseq-master/Makefile -@@ -22,6 +22,10 @@ ifndef ROOT - ROOT = $(shell pwd) - endif - -+ifndef PREFIX -+PREFIX = $(ROOT) -+endif -+ - ifndef SMITHLAB_CPP - SMITHLAB_CPP=$(ROOT)/smithlab_cpp/ - endif -@@ -91,8 +95,8 @@ endif - $(CXX) $(CXXFLAGS) -o $@ $^ $(INCLUDEARGS) $(LIBS) - - install: $(PROGS) -- @mkdir -p $(ROOT)/bin -- @install -m 755 $(PROGS) $(ROOT)/bin -+ @mkdir -p $(PREFIX)/bin -+ @install -m 755 $(PROGS) $(PREFIX)/bin - - clean: - @-rm -f $(PROGS) *.o *~ diff --git a/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch b/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch deleted file mode 100644 index 035a3b1fe4..0000000000 --- a/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch +++ /dev/null @@ -1,33 +0,0 @@ -This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15 - -From a937a54d56e8a6ff06237471e568154d1fa5f267 Mon Sep 17 00:00:00 2001 -From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> -Date: Thu, 25 Jun 2015 15:02:35 +0200 -Subject: [PATCH] Link with libbam.a if provided via LIBBAM - ---- - Makefile | 7 +++++++ - 1 file changed, 7 insertions(+) - -diff --git a/Makefile b/Makefile -index e334f2f..de310e4 100644 ---- a/preseq-master/Makefile -+++ b/preseq-master/Makefile -@@ -83,10 +83,17 @@ $(PROGS): $(addprefix $(SMITHLAB_CPP)/, \ - preseq: continued_fraction.o load_data_for_complexity.o moment_sequence.o - - ifdef SAMTOOLS_DIR -+ifdef LIBBAM -+LIBS += -pthread -+bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \ -+ $(LIBBAM) -+else - bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \ - $(addprefix $(SAMTOOLS_DIR)/, sam.o bam.o bam_import.o bam_pileup.o \ - faidx.o bam_aux.o kstring.o knetfile.o sam_header.o razf.o bgzf.o) - endif -+endif # SAMTOOLS_DIR -+ - - %.o: %.cpp %.hpp - $(CXX) $(CXXFLAGS) -c -o $@ $< $(INCLUDEARGS) |