New package ARC

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: New package ARC
From: zmsaif <zmsaif%nmsu.edu@localhost>
Date: Tue, 24 Oct 2017 20:59:56 +0000
Module Name:	pkgsrc-wip
Committed By:	zmsaif <zmsaif%nmsu.edu@localhost>
Pushed By:	zmsaif
Date:		Tue Oct 24 14:59:56 2017 -0600
Changeset:	9a642f7a7650f0e6cb6d223399ca3c24c1514cab

Added Files:
	ARC/DESCR
	ARC/Makefile
	ARC/PLIST
	ARC/distinfo
	ARC/patches/patch-test__data_runarc

Log Message:
New package ARC

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=9a642f7a7650f0e6cb6d223399ca3c24c1514cab

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 ARC/DESCR                           | 20 +++++++++++
 ARC/Makefile                        | 56 ++++++++++++++++++++++++++++++
 ARC/PLIST                           | 69 +++++++++++++++++++++++++++++++++++++
 ARC/distinfo                        |  7 ++++
 ARC/patches/patch-test__data_runarc | 13 +++++++
 5 files changed, 165 insertions(+)

diffs:
diff --git a/ARC/DESCR b/ARC/DESCR
new file mode 100644
index 0000000000..aa0ffa960b
--- /dev/null
+++ b/ARC/DESCR
@@ -0,0 +1,20 @@
+ARC -- Assembly by Reduced Complexity
+
+ARC is a pipeline which facilitates iterative, reference-guided de
+novo assemblies with the intent of:
+
+- Reducing time in analysis and increasing accuracy of results by only
+  considering those reads which should assemble together.
+
+- Reducing/removing reference bias as compared to mapping-based
+  approaches.
+
+The software is designed to work in situations where a whole-genome
+assembly is not the objective, but rather when the researcher wishes
+to assemble discrete 'targets' contained within next-generation
+shotgun sequence data. ARC decomplexifies the traditionally difficult
+problem of assembly by breaking the reads into small, manageable
+subsets which can then be assembled quickly and efficiently in
+parallel. Applications include those in which the researcher wishes to
+de novo assemble specific content and a set of semi-similar reference
+targets is available to initialize the assembly process.
diff --git a/ARC/Makefile b/ARC/Makefile
new file mode 100644
index 0000000000..6f92201964
--- /dev/null
+++ b/ARC/Makefile
@@ -0,0 +1,56 @@
+# $NetBSD$
+
+PKGNAME=	ARC-1.1.4
+DISTNAME=	ibest-ARC-v1.1.4-beta-0-g3831cb8
+CATEGORIES=	biology
+MASTER_SITES=   ${MASTER_SITE_GITHUB:=ibest/ARC/tarball/master/}
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	http://ibest.github.io/ARC/
+COMMENT=	Genomics pipeline for de novo assemblies
+LICENSE=	apache-2.0
+
+WRKSRC=		${WRKDIR}/ibest-ARC-3831cb8
+USE_TOOLS+=	pax
+USE_LANGUAGES=	# none
+PYDISTUTILSPKG=	yes
+
+REPLACE_PYTHON+=	ARC/exceptions.py
+REPLACE_PYTHON+=	ARC/runners/assembly_checker.py
+REPLACE_PYTHON+=	ARC/runners/__init__.py
+REPLACE_PYTHON+=	ARC/runners/base.py
+REPLACE_PYTHON+=	ARC/runners/mapper.py
+REPLACE_PYTHON+=	ARC/runners/finisher.py
+REPLACE_PYTHON+=	ARC/runners/assembler.py
+REPLACE_PYTHON+=	ARC/__init__.py
+REPLACE_PYTHON+=	ARC/logger.py
+REPLACE_PYTHON+=	ARC/queue.py
+REPLACE_PYTHON+=	ARC/app.py
+REPLACE_PYTHON+=	ARC/process_runner.py
+REPLACE_PYTHON+=	ARC/spawn.py
+REPLACE_PYTHON+=	ARC/config.py
+REPLACE_PYTHON+=	ARC/functions.py
+REPLACE_PYTHON+=        bin/ARC
+REPLACE_PYTHON+=	test_data/unit_tests.py
+
+DEPENDS+=	blat>=3.5:../../biology/blat
+DEPENDS+=	SPAdes>=3.8.2:../../biology/SPAdes
+DEPENDS+=	bowtie2>=2.2.9:../../biology/bowtie2
+DEPENDS+=	${PYPKGPREFIX}-biopython>=1.63b:../../biology/py-biopython
+DEPENDS+=	${PYPKGPREFIX}-sqlite3>=${PY_DISTVERSION}:../../databases/py-sqlite3
+
+INSTALLATION_DIRS+=	share/doc/ARC share/examples/ARC
+NONEXECUTABLE_FILES+=	test_data/clean test_data/runarc
+
+post-extract:
+.for f in ${NONEXECUTABLE_FILES}
+	${CHMOD} a-x ${WRKSRC}/${f}
+.endfor
+
+post-install:
+	${INSTALL_DATA} ${WRKSRC}/docs/Pipeline.pdf ${DESTDIR}${PREFIX}/share/doc/ARC
+	cd ${WRKSRC}/test_data && ${PAX} -rw . ${DESTDIR}${PREFIX}/share/examples/ARC
+	${RM} -f ${DESTDIR}${PREFIX}/share/examples/ARC/runarc.orig
+
+.include "../../lang/python/application.mk"
+.include "../../lang/python/extension.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/ARC/PLIST b/ARC/PLIST
new file mode 100644
index 0000000000..ef8e58c5cf
--- /dev/null
+++ b/ARC/PLIST
@@ -0,0 +1,69 @@
+@comment $NetBSD$
+bin/ARC
+${PYSITELIB}/ARC/__init__.py
+${PYSITELIB}/ARC/__init__.pyc
+${PYSITELIB}/ARC/__init__.pyo
+${PYSITELIB}/ARC/app.py
+${PYSITELIB}/ARC/app.pyc
+${PYSITELIB}/ARC/app.pyo
+${PYSITELIB}/ARC/config.py
+${PYSITELIB}/ARC/config.pyc
+${PYSITELIB}/ARC/config.pyo
+${PYSITELIB}/ARC/exceptions.py
+${PYSITELIB}/ARC/exceptions.pyc
+${PYSITELIB}/ARC/exceptions.pyo
+${PYSITELIB}/ARC/functions.py
+${PYSITELIB}/ARC/functions.pyc
+${PYSITELIB}/ARC/functions.pyo
+${PYSITELIB}/ARC/logger.py
+${PYSITELIB}/ARC/logger.pyc
+${PYSITELIB}/ARC/logger.pyo
+${PYSITELIB}/ARC/process_runner.py
+${PYSITELIB}/ARC/process_runner.pyc
+${PYSITELIB}/ARC/process_runner.pyo
+${PYSITELIB}/ARC/queue.py
+${PYSITELIB}/ARC/queue.pyc
+${PYSITELIB}/ARC/queue.pyo
+${PYSITELIB}/ARC/runners/__init__.py
+${PYSITELIB}/ARC/runners/__init__.pyc
+${PYSITELIB}/ARC/runners/__init__.pyo
+${PYSITELIB}/ARC/runners/assembler.py
+${PYSITELIB}/ARC/runners/assembler.pyc
+${PYSITELIB}/ARC/runners/assembler.pyo
+${PYSITELIB}/ARC/runners/assembly_checker.py
+${PYSITELIB}/ARC/runners/assembly_checker.pyc
+${PYSITELIB}/ARC/runners/assembly_checker.pyo
+${PYSITELIB}/ARC/runners/base.py
+${PYSITELIB}/ARC/runners/base.pyc
+${PYSITELIB}/ARC/runners/base.pyo
+${PYSITELIB}/ARC/runners/finisher.py
+${PYSITELIB}/ARC/runners/finisher.pyc
+${PYSITELIB}/ARC/runners/finisher.pyo
+${PYSITELIB}/ARC/runners/mapper.py
+${PYSITELIB}/ARC/runners/mapper.pyc
+${PYSITELIB}/ARC/runners/mapper.pyo
+${PYSITELIB}/ARC/spawn.py
+${PYSITELIB}/ARC/spawn.pyc
+${PYSITELIB}/ARC/spawn.pyo
+share/doc/ARC/Pipeline.pdf
+share/examples/ARC/ARC_config.txt
+share/examples/ARC/clean
+share/examples/ARC/reads/RNA_seq_Sample.fasta
+share/examples/ARC/reads/RNA_seq_Sample.fastq
+share/examples/ARC/reads/Sample1_R1.fasta
+share/examples/ARC/reads/Sample1_R1.fastq
+share/examples/ARC/reads/Sample1_R2.fasta
+share/examples/ARC/reads/Sample1_R2.fastq
+share/examples/ARC/reads/Sample1_SE.fasta
+share/examples/ARC/reads/Sample1_SE.fastq
+share/examples/ARC/reads/Sample2_R1.fasta
+share/examples/ARC/reads/Sample2_R1.fastq
+share/examples/ARC/reads/Sample2_R2.fasta
+share/examples/ARC/reads/Sample2_R2.fastq
+share/examples/ARC/reads/Sample2_SE.fasta
+share/examples/ARC/reads/Sample2_SE.fastq
+share/examples/ARC/reads/repeat_reads.fasta
+share/examples/ARC/reads/repeat_reads.fastq
+share/examples/ARC/runarc
+share/examples/ARC/targets.fa
+share/examples/ARC/unit_tests.py
diff --git a/ARC/distinfo b/ARC/distinfo
new file mode 100644
index 0000000000..2ac24b88f3
--- /dev/null
+++ b/ARC/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (ibest-ARC-v1.1.4-beta-0-g3831cb8.tar.gz) = 55452b86afb3f765a9cdb12f495272866320ba4c
+RMD160 (ibest-ARC-v1.1.4-beta-0-g3831cb8.tar.gz) = bb51afbcf0bb42dd29b23d3e0e08d10c6948a251
+SHA512 (ibest-ARC-v1.1.4-beta-0-g3831cb8.tar.gz) = 8fe359d592e4f600c353ffa3881b717f270d51b63c4ac481003e81b70d78bc3a7834ec20ee5425a1950b77bed7054f559c728576719e8889e495ad181e126a62
+Size (ibest-ARC-v1.1.4-beta-0-g3831cb8.tar.gz) = 627297 bytes
+SHA1 (patch-test__data_runarc) = b0d3804e0732a7a088566bc72ba07fcef017ebda
diff --git a/ARC/patches/patch-test__data_runarc b/ARC/patches/patch-test__data_runarc
new file mode 100644
index 0000000000..b95ef81d07
--- /dev/null
+++ b/ARC/patches/patch-test__data_runarc
@@ -0,0 +1,13 @@
+$NetBSD$
+
+Change path to ARC binary.
+
+--- test_data/runarc.orig	2016-03-29 05:17:16.000000000 +0000
++++ test_data/runarc
+@@ -1,5 +1,5 @@
+ #rm -rf working*
+ #rm -rf finished_*
+ echo "See log.txt for output...."
+-time ../bin/ARC --debug > log.txt
++time ARC --debug > log.txt
+ # > runarc.log
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