gnu: Add preseq.
* gnu/packages/bioinformatics.scm (preseq): New variable. * gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: New file. * gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: New file. * gnu-system.am (dist_patch_DATA): Add them.
This commit is contained in:
Ricardo Wurmus
parent
5bdda30b32
commit
56e373ef75
4 changed files with 128 additions and 0 deletions
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@ -571,6 +571,8 @@ dist_patch_DATA = \
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gnu/packages/patches/plotutils-libpng-jmpbuf.patch \
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gnu/packages/patches/polkit-drop-test.patch \
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gnu/packages/patches/portaudio-audacity-compat.patch \
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gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch \
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gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch \
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gnu/packages/patches/procps-make-3.82.patch \
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gnu/packages/patches/pt-scotch-build-parallelism.patch \
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gnu/packages/patches/pulseaudio-fix-mult-test.patch \
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@ -2087,6 +2087,62 @@ subsequent visualization, annotation and storage of results.")
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;; LGPLv2.1+
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(license (list license:gpl2 license:lgpl2.1+))))
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(define-public preseq
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(package
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(name "preseq")
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(version "1.0.2")
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(source (origin
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(method url-fetch)
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(uri
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(string-append "http://smithlabresearch.org/downloads/preseq-"
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version ".tar.bz2"))
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(sha256
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(base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc"))
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(patches (list (search-patch "preseq-1.0.2-install-to-PREFIX.patch")
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(search-patch "preseq-1.0.2-link-with-libbam.patch")))
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(modules '((guix build utils)))
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(snippet
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;; Remove bundled samtools.
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'(delete-file-recursively "preseq-master/samtools"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ;no "check" target
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#:phases
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(modify-phases %standard-phases
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(add-after
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'unpack 'enter-dir
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(lambda _
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(chdir "preseq-master")
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#t))
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(add-after
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'unpack 'use-samtools-headers
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(lambda _
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(substitute* '("smithlab_cpp/SAM.cpp"
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"smithlab_cpp/SAM.hpp")
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(("sam.h") "samtools/sam.h"))
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#t))
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(delete 'configure))
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#:make-flags (list (string-append "PREFIX="
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(assoc-ref %outputs "out"))
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(string-append "LIBBAM="
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(assoc-ref %build-inputs "samtools")
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"/lib/libbam.a"))))
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(inputs
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`(("gsl" ,gsl)
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("samtools" ,samtools-0.1)
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("zlib" ,zlib)))
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(home-page "http://smithlabresearch.org/software/preseq/")
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(synopsis "Program for analyzing library complexity")
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(description
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"The preseq package is aimed at predicting and estimating the complexity
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of a genomic sequencing library, equivalent to predicting and estimating the
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number of redundant reads from a given sequencing depth and how many will be
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expected from additional sequencing using an initial sequencing experiment.
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The estimates can then be used to examine the utility of further sequencing,
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optimize the sequencing depth, or to screen multiple libraries to avoid low
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complexity samples.")
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(license license:gpl3+)))
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(define-public sra-tools
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(package
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(name "sra-tools")
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37
gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
Normal file
37
gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch
Normal file
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@ -0,0 +1,37 @@
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This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15
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From 65387b0d766e6c06a15cf8d8f9183d9a4ba644bb Mon Sep 17 00:00:00 2001
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From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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Date: Thu, 25 Jun 2015 15:01:53 +0200
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Subject: [PATCH] Install to PREFIX
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---
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Makefile | 8 ++++++--
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1 file changed, 6 insertions(+), 2 deletions(-)
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diff --git a/Makefile b/Makefile
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index 4d0367a..e334f2f 100644
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--- a/preseq-master/Makefile
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+++ b/preseq-master/Makefile
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@@ -22,6 +22,10 @@ ifndef ROOT
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ROOT = $(shell pwd)
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endif
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+ifndef PREFIX
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+PREFIX = $(ROOT)
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+endif
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+
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ifndef SMITHLAB_CPP
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SMITHLAB_CPP=$(ROOT)/smithlab_cpp/
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endif
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@@ -91,8 +95,8 @@ endif
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$(CXX) $(CXXFLAGS) -o $@ $^ $(INCLUDEARGS) $(LIBS)
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install: $(PROGS)
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- @mkdir -p $(ROOT)/bin
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- @install -m 755 $(PROGS) $(ROOT)/bin
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+ @mkdir -p $(PREFIX)/bin
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+ @install -m 755 $(PROGS) $(PREFIX)/bin
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clean:
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@-rm -f $(PROGS) *.o *~
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33
gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
Normal file
33
gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch
Normal file
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@ -0,0 +1,33 @@
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This patch has been submitted upstream: https://github.com/smithlabcode/preseq/pull/15
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From a937a54d56e8a6ff06237471e568154d1fa5f267 Mon Sep 17 00:00:00 2001
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From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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Date: Thu, 25 Jun 2015 15:02:35 +0200
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Subject: [PATCH] Link with libbam.a if provided via LIBBAM
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---
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Makefile | 7 +++++++
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1 file changed, 7 insertions(+)
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diff --git a/Makefile b/Makefile
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index e334f2f..de310e4 100644
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--- a/preseq-master/Makefile
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+++ b/preseq-master/Makefile
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@@ -83,10 +83,17 @@ $(PROGS): $(addprefix $(SMITHLAB_CPP)/, \
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preseq: continued_fraction.o load_data_for_complexity.o moment_sequence.o
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ifdef SAMTOOLS_DIR
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+ifdef LIBBAM
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+LIBS += -pthread
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+bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \
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+ $(LIBBAM)
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+else
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bam2mr preseq: $(addprefix $(SMITHLAB_CPP)/, SAM.o) \
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$(addprefix $(SAMTOOLS_DIR)/, sam.o bam.o bam_import.o bam_pileup.o \
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faidx.o bam_aux.o kstring.o knetfile.o sam_header.o razf.o bgzf.o)
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endif
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+endif # SAMTOOLS_DIR
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+
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%.o: %.cpp %.hpp
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$(CXX) $(CXXFLAGS) -c -o $@ $< $(INCLUDEARGS)
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