[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
[Gsrc-commit] trunk r7870: bunch of bio programs
|
From: |
Carl Hansen |
|
Subject: |
[Gsrc-commit] trunk r7870: bunch of bio programs |
|
Date: |
Wed, 27 Oct 2021 03:04:21 -0400 (EDT) |
|
User-agent: |
Bazaar (2.7.0dev1) |
------------------------------------------------------------
revno: 7870
revision-id: carlhansen1234@gmail.com-20211027070410-79kcxcbfg2h7byij
parent: carlhansen1234@gmail.com-20211027005051-04pczx4iwovgppzo
committer: carlhansen1234@gmail.com
branch nick: trunk
timestamp: Wed 2021-10-27 00:04:10 -0700
message:
bunch of bio programs
added:
pkg/bio/bcftools/ bcftools-20211027035004-c4quco8a79mnagtx-1
pkg/bio/bcftools/Makefile makefile-20211027035004-c4quco8a79mnagtx-3
pkg/bio/bcftools/config.mk config.mk-20211027035004-c4quco8a79mnagtx-2
pkg/bio/bcftools/sha256sums sha256sums-20211027035004-c4quco8a79mnagtx-4
pkg/bio/dwgsim/ dwgsim-20211027070334-afi11688wscfnytz-1
pkg/bio/dwgsim/Makefile makefile-20211027070334-afi11688wscfnytz-3
pkg/bio/dwgsim/config.mk config.mk-20211027070334-afi11688wscfnytz-2
pkg/bio/dwgsim/sha256sums sha256sums-20211027070334-afi11688wscfnytz-4
modified:
pkg/bio/bfast/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-75
pkg/bio/htslib/Makefile makefile-20160617200040-lqf8h520dfq0rtk7-49
pkg/bio/htslib/sha256sums sha256sums-20160617200040-lqf8h520dfq0rtk7-50
pkg/bio/samtools/Makefile makefile-20160617195624-kwz1a09vkg4le6fu-176
pkg/bio/samtools/sha256sums sha256sums-20160617195624-kwz1a09vkg4le6fu-177
=== added directory 'pkg/bio/bcftools'
=== added file 'pkg/bio/bcftools/Makefile'
--- a/pkg/bio/bcftools/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bcftools/Makefile 2021-10-27 07:04:10 +0000
@@ -0,0 +1,69 @@
+# Copyright ©2021 Carl Hansen <carlhansen@gnu.org>
+#
+# This file is part of BioSRC and GSRC. the GNU Source Release Collection.
+# http://www.gnu.org/software/gsrc
+#
+# BioSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# BioSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+#
+#
+# Send bug reports and comments about GSRC problems to bug-gsrc@gnu.org
+
+NAME = bcftools
+GARNAME = bcftools
+GARVERSION = 1.14
+HOME_URL = http://https://www.htslib.org/download/
+DESCRIPTION = BCFtools, utilities that manipulate variant calls in the Variant
Call Format (VCF)
+define BLURB
+BCFtools is a set of utilities that manipulate variant calls in the
+Variant Call Format (VCF) and its binary counterpart BCF. All commands
+work transparently with both VCFs and BCFs, both uncompressed and
+BGZF-compressed.
+endef
+LICENSE = Expat License
+CITE = https://doi.org/10.1093/gigascience/giab008
+######################################################################
+#https://github.com/samtools/bcftools/releases/download/1.14/bcftools-1.14.tar.bz2
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = samtools/$(GARNAME)/releases/download/$(GARVERSION)/
+DISTFILES = $(DISTNAME).tar.bz2
+#BUILD_SCRIPTS = $(WORKSRC)/Makefile
+#INSTALL_SCRIPTS = $(WORKSRC)/Makefile lib headers #programs lib headers man
+
+BUILDDEPS =
+LIBDEPS =
+# apt install libbz2-1.0 libbz2-dev
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
+export DESTDIR= $(packageprefix)/packages/$(PACKAGENAME)
+
+pre-install: build
+ mkdir -p $(packageprefix)/packages/$(PACKAGENAME)
+ mkdir -p $(prefix)/packages/$(PACKAGENAME)
+
+
+#INSTALL_ARGS += prefix=$(packageprefix)
+#
+#install-lib:
+# @printf "[$(OK)install$(OFF)] $(MSG)Installing libbam.$(OFF)\n"
+# $(INSTALL_LIB) $(WORKSRC)/libbam.a
+# $(MAKECOOKIE)
+#
+#install-headers:
+# install -d $(packageprefix)/include/bam
+# for f in $(WORKSRC)/*.h; do \
+# install -m644 $$f $(packageprefix)/include/bam/`basename $$f`; \
+# done
+# $(MAKECOOKIE)
=== added file 'pkg/bio/bcftools/config.mk'
--- a/pkg/bio/bcftools/config.mk 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bcftools/config.mk 2021-10-27 07:04:10 +0000
@@ -0,0 +1,4 @@
+## Configuration options
+
+CONFIGURE_OPTS ?=
+BUILD_OPTS ?=
=== added file 'pkg/bio/bcftools/sha256sums'
--- a/pkg/bio/bcftools/sha256sums 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/bcftools/sha256sums 2021-10-27 07:04:10 +0000
@@ -0,0 +1,1 @@
+b7ef88ae89fcb55658c5bea2e8cb8e756b055e13860036d6be13756782aa19cb
download/bcftools-1.14.tar.bz2
=== modified file 'pkg/bio/bfast/Makefile'
--- a/pkg/bio/bfast/Makefile 2018-06-30 06:50:19 +0000
+++ b/pkg/bio/bfast/Makefile 2021-10-27 07:04:10 +0000
@@ -18,7 +18,7 @@
NAME = BFAST
GARNAME = bfast
GARVERSION = 0.7.0a
-HOME_URL = https://sourceforge.net/projects/bfast/
+HOME_URL = https://github.com/nh13/bfast
DESCRIPTION = Blat-like Fast Accurate Search Tool
define BLURB
BFAST is a tool for mapping short reads to reference sequences. Its
@@ -34,7 +34,7 @@
DISTFILES = $(DISTNAME).tar.gz
SIGFILES =
-BUILDDEPS = bowtie2
+BUILDDEPS =# bowtie2
LIBDEPS =
######################################################################
=== added directory 'pkg/bio/dwgsim'
=== added file 'pkg/bio/dwgsim/Makefile'
--- a/pkg/bio/dwgsim/Makefile 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/dwgsim/Makefile 2021-10-27 07:04:10 +0000
@@ -0,0 +1,78 @@
+# Copyright © 2013, 2014 Brandon Invergo <brandon@invergo.net>
+# Copyright © 2021 Carl Hansen <carlhansen@gnu.org>
+#
+# This file is part of GSRC, the GNU Source Release Collection.
+# http://www.gnu.org/software/gsrc
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+
+# Send bug reports and comments about GSRC problems to bug-gsrc@gnu.org
+
+NAME = DWGSIM
+GARNAME = dwgsim
+GARVERSION = 0.1.12
+HOME_URL = http://github.com/nh13/DWGSIM
+DESCRIPTION = Whole Genome Simulator for Next-Generation Sequencing
+define BLURB
+Whole genome simulation can be performed with dwgsim. dwgsim is based on
+wgsim found in SAMtools written by Heng Li, and forked from DNAA. It was
+modified to handle ABI SOLiD and Ion Torrent data, as well as various
+assumptions about aligners and positions of indels. No longer under
+development
+endef
+LICENSE = GPLv2
+CITE =
+
+######################################################################
+# https://github.com/nh13/DWGSIM/archive/refs/tags/dwgsim.0.1.12.tar.gz
+# https://github.com/nh13/DWGSIM.git
+#git clone --recursive
+MASTER_SITES = $(MASTER_GITHUB_GIT)
+MASTER_SUBDIR = nh13/
+GIT_PATH = $(MASTER_SITES)$(MASTER_SUBDIR)$(GARNAME).git
+
+DISTFILES = $(GARNAME).$(GARVERSION).tar.gz
+NOCHECKSUM = $(DISTFILES)
+SIGFILES =
+
+GIT_REVISION =
+
+BUILDDEPS = samtools
+LIBDEPS =
+
+CONFIGURE_SCRIPTS =
+BUILD_SCRIPTS = my
+######################################################################
+
+include ../../../gar/gar.lib/auto.mk
+include config.mk
+
+fetch-my:
+ mkdir -p $(DOWNLOADDIR)/git
+ cd $(DOWNLOADDIR)/git && \
+ git clone --recursive $(GIT_PATH) $(DISTNAME) && \
+ (cd $(DISTNAME) && git checkout $(GIT_REVISION)) && \
+ tar czvf ../$(notdir $*) $(DISTNAME)
+ $(MAKECOOKIE)
+
+
+build-my:
+ cd $(WORKSRC)/samtools && git submodule init
+ cd $(WORKSRC)/samtools && git submodule update
+ $(MAKE) -C $(WORKSRC)
+ $(MAKECOOKIE)
+
+install:
+ echo not done yet
+
=== added file 'pkg/bio/dwgsim/config.mk'
--- a/pkg/bio/dwgsim/config.mk 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/dwgsim/config.mk 2021-10-27 07:04:10 +0000
@@ -0,0 +1,4 @@
+## Configuration options
+
+CONFIGURE_OPTS ?=
+BUILD_OPTS ?=
=== added file 'pkg/bio/dwgsim/sha256sums'
=== modified file 'pkg/bio/htslib/Makefile'
--- a/pkg/bio/htslib/Makefile 2018-03-14 05:45:56 +0000
+++ b/pkg/bio/htslib/Makefile 2021-10-27 07:04:10 +0000
@@ -1,6 +1,8 @@
# Copyright © 2013, 2014 Brandon Invergo <brandon@invergo.net>
+# Copyright © 2021 Carl Hansen <carlhansen@gnu.org>
#
-# This file is part of GSRC.
+# This file is part of GSRC, the GNU Source Release Collection.
+# http://www.gnu.org/software/gsrc
#
# GSRC is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
@@ -14,10 +16,13 @@
#
# You should have received a copy of the GNU General Public License
# along with GSRC. If not, see <http://www.gnu.org/licenses/>.
+#
+#
+# Send bug reports and comments about GSRC problems to bug-gsrc@gnu.org
NAME = HTSlib
GARNAME = htslib
-GARVERSION = 1.0
+GARVERSION = 1.14
HOME_URL = https://github.com/samtools/htslib
DESCRIPTION = C library for high-throughput sequencing data formats
define BLURB
@@ -28,19 +33,20 @@
CITE =
######################################################################
-#https://github.com/samtools/htslib/archive/develop.zip
-MASTER_SITES = $(MASTER_SOURCEFORGE)
-MASTER_SUBDIR = samtools/files/samtools/$(GARVERSION)/
+#https://github.com/samtools/htslib/releases/download/1.14/htslib-1.14.tar.bz2
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = samtools/$(GARNAME)/releases/download/$(GARVERSION)/
DISTFILES = $(DISTNAME).tar.bz2
-BUILD_SCRIPTS = $(WORKSRC)/Makefile
-INSTALL_SCRIPTS = $(WORKSRC)/Makefile
+#BUILD_SCRIPTS = $(WORKSRC)/Makefile
+#INSTALL_SCRIPTS = $(WORKSRC)/Makefile
BUILDDEPS =
LIBDEPS =
######################################################################
-include ../../../gar/gar.mk
+include ../../../gar/gar.lib/auto.mk
include config.mk
#INSTALL_ARGS = prefix=$(packageprefix)
+
=== modified file 'pkg/bio/htslib/sha256sums'
--- a/pkg/bio/htslib/sha256sums 2016-06-17 20:01:53 +0000
+++ b/pkg/bio/htslib/sha256sums 2021-10-27 07:04:10 +0000
@@ -1,1 +1,1 @@
-3d53fb081fafd930cadfee6f950faacc1993a0f4a9fa329fc897865fc6b331bc
download/htslib-1.0.tar.bz2
+ed221b8f52f4812f810eebe0cc56cd8355a5c9d21c62d142ac05ad0da147935f
download/htslib-1.14.tar.bz2
=== modified file 'pkg/bio/samtools/Makefile'
--- a/pkg/bio/samtools/Makefile 2018-06-30 06:57:51 +0000
+++ b/pkg/bio/samtools/Makefile 2021-10-27 07:04:10 +0000
@@ -1,7 +1,8 @@
# Copyright © 2014 Brandon Invergo <brandon@invergo.net>
-# Copyright © 2017 Carl Hansen <carlhansen@gnu.org>
+# Copyright © 2017, 2021 Carl Hansen <carlhansen@gnu.org>
#
-# This file is part of BioSRC and GSRC.
+# This file is part of BioSRC and GSRC. the GNU Source Release Collection.
+# http://www.gnu.org/software/gsrc
#
# BioSRC is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
@@ -15,11 +16,14 @@
#
# You should have received a copy of the GNU General Public License
# along with BioSRC. If not, see <http://www.gnu.org/licenses/>.
+#
+#
+# Send bug reports and comments about GSRC problems to bug-gsrc@gnu.org
NAME = SAMtools
GARNAME = samtools
-GARVERSION = 1.5
-HOME_URL = http://samtools.sourceforge.net/
+GARVERSION = 1.14
+HOME_URL = http://https://www.htslib.org/download/
DESCRIPTION = Utilities for manipulating alignments in the SAM format
define BLURB
SAMtools provides utilities for manipulating alignments in the SAM
@@ -31,31 +35,37 @@
CITE = doi:10.1093/bioinformatics/btp352
######################################################################
-
-MASTER_SITES = $(MASTER_SOURCEFORGE)
-MASTER_SUBDIR = $(GARNAME)/files/$(GARNAME)/$(GARVERSION)/
+#
https://github.com/samtools/samtools/releases/download/1.14/samtools-1.14.tar.bz2
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = $(GARNAME)/$(GARNAME)/releases/download/$(GARVERSION)/
DISTFILES = $(DISTNAME).tar.bz2
-BUILD_SCRIPTS = $(WORKSRC)/Makefile
-INSTALL_SCRIPTS = $(WORKSRC)/Makefile lib headers #programs lib headers man
+#BUILD_SCRIPTS = $(WORKSRC)/Makefile
+#INSTALL_SCRIPTS = $(WORKSRC)/Makefile lib headers #programs lib headers man
BUILDDEPS =
LIBDEPS =
# apt install libbz2-1.0 libbz2-dev
######################################################################
-include ../../../gar/gar.mk
+include ../../../gar/gar.lib/auto.mk
include config.mk
-
-INSTALL_ARGS += prefix=$(packageprefix)
-
-install-lib:
- @printf "[$(OK)install$(OFF)] $(MSG)Installing libbam.$(OFF)\n"
- $(INSTALL_LIB) $(WORKSRC)/libbam.a
- $(MAKECOOKIE)
-
-install-headers:
- install -d $(packageprefix)/include/bam
- for f in $(WORKSRC)/*.h; do \
- install -m644 $$f $(packageprefix)/include/bam/`basename $$f`; \
- done
- $(MAKECOOKIE)
+export DESTDIR= $(packageprefix)/packages/$(PACKAGENAME)
+
+pre-install: build
+ mkdir -p $(packageprefix)/packages/$(PACKAGENAME)
+ mkdir -p $(prefix)/packages/$(PACKAGENAME)
+
+
+#INSTALL_ARGS += prefix=$(packageprefix)
+#
+#install-lib:
+# @printf "[$(OK)install$(OFF)] $(MSG)Installing libbam.$(OFF)\n"
+# $(INSTALL_LIB) $(WORKSRC)/libbam.a
+# $(MAKECOOKIE)
+#
+#install-headers:
+# install -d $(packageprefix)/include/bam
+# for f in $(WORKSRC)/*.h; do \
+# install -m644 $$f $(packageprefix)/include/bam/`basename $$f`; \
+# done
+# $(MAKECOOKIE)
=== modified file 'pkg/bio/samtools/sha256sums'
--- a/pkg/bio/samtools/sha256sums 2017-09-23 04:22:17 +0000
+++ b/pkg/bio/samtools/sha256sums 2021-10-27 07:04:10 +0000
@@ -1,1 +1,1 @@
-8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6
download/samtools-1.5.tar.bz2
+9341dabaa98b0ea7d60fd47e42af25df43a7d3d64d8e654cdf852974546b7d74
download/samtools-1.14.tar.bz2
| [Prev in Thread] |
Current Thread |
[Next in Thread] |
- [Gsrc-commit] trunk r7870: bunch of bio programs,
Carl Hansen <=