diff options
| -rw-r--r-- | gnu-system.am | 2 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 56 | ||||
| -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 |
4 files changed, 128 insertions, 0 deletions
diff --git a/gnu-system.am b/gnu-system.am index 11ae3e630c..59090b5475 100644 --- a/gnu-system.am +++ b/gnu-system.am @@ -571,6 +571,8 @@ 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 \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f6349cfb8f..2b7f78be34 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2087,6 +2087,62 @@ subsequent visualization, annotation and storage of results.") ;; LGPLv2.1+ (license (list license:gpl2 license:lgpl2.1+)))) +(define-public preseq + (package + (name "preseq") + (version "1.0.2") + (source (origin + (method url-fetch) + (uri + (string-append "http://smithlabresearch.org/downloads/preseq-" + version ".tar.bz2")) + (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"))) + (modules '((guix build utils))) + (snippet + ;; Remove bundled samtools. + '(delete-file-recursively "preseq-master/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 + 'unpack '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")))) + (inputs + `(("gsl" ,gsl) + ("samtools" ,samtools-0.1) + ("zlib" ,zlib))) + (home-page "http://smithlabresearch.org/software/preseq/") + (synopsis "Program for analyzing library complexity") + (description + "The preseq package is aimed at predicting and estimating the complexity +of a genomic sequencing library, equivalent to predicting and estimating the +number of redundant reads from a given sequencing depth and how many will be +expected from additional sequencing using an initial sequencing experiment. +The estimates can then be used to examine the utility of further sequencing, +optimize the sequencing depth, or to screen multiple libraries to avoid low +complexity samples.") + (license license:gpl3+))) + (define-public sra-tools (package (name "sra-tools") 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 new file mode 100644 index 0000000000..f8318ae0f5 --- /dev/null +++ b/gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch @@ -0,0 +1,37 @@ +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 new file mode 100644 index 0000000000..035a3b1fe4 --- /dev/null +++ b/gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch @@ -0,0 +1,33 @@ +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) |