M gnu-system.am => gnu-system.am +0 -2
@@ 657,8 657,6 @@ dist_patch_DATA = \
gnu/packages/patches/plotutils-libpng-jmpbuf.patch \
gnu/packages/patches/polkit-drop-test.patch \
gnu/packages/patches/portaudio-audacity-compat.patch \
- gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch \
- gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch \
gnu/packages/patches/procps-make-3.82.patch \
gnu/packages/patches/pt-scotch-build-parallelism.patch \
gnu/packages/patches/pulseaudio-fix-mult-test.patch \
M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +18 -25
@@ 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")
D gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch => gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch +0 -37
@@ 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 *~
D gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch => gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch +0 -33
@@ 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)