pkgsrc/biology/Makefile

# $NetBSD: Makefile,v 1.55 2019/08/09 21:52:34 brook Exp $
#

COMMENT=	Software for the biological sciences

SUBDIR+=	arka
SUBDIR+=	azara
SUBDIR+=	bcftools
SUBDIR+=	bioperl
SUBDIR+=	bodr
SUBDIR+=	bwa
SUBDIR+=	canu
SUBDIR+=	cdhit
SUBDIR+=	chemical-mime-data
SUBDIR+=	chemtool
SUBDIR+=	clustalw
SUBDIR+=	coalesce
SUBDIR+=	fastDNAml
SUBDIR+=	fastp
SUBDIR+=	fluctuate
SUBDIR+=	gabedit
SUBDIR+=	genesplicer
SUBDIR+=	glimmer
SUBDIR+=	gnome-chemistry-utils
SUBDIR+=	gp
SUBDIR+=	gromacs
SUBDIR+=	hisat2
SUBDIR+=	hmmer
SUBDIR+=	htslib
SUBDIR+=	kallisto
SUBDIR+=	lucy
SUBDIR+=	mopac
SUBDIR+=	mpqc
SUBDIR+=	mummer
SUBDIR+=	ncbi-blast+
SUBDIR+=	nut
SUBDIR+=	openbabel
SUBDIR+=	p5-Bio-ASN1-EntrezGene
SUBDIR+=	pdbalign
SUBDIR+=	phylip
SUBDIR+=	plink
SUBDIR+=	plinkseq
SUBDIR+=	primer3
SUBDIR+=	profit
SUBDIR+=	puzzle
SUBDIR+=	py-biopython
SUBDIR+=	py-mol
SUBDIR+=	py-pydicom
SUBDIR+=	rasmol
SUBDIR+=	samtools
SUBDIR+=	sewer
SUBDIR+=	stacks
SUBDIR+=	stride
SUBDIR+=	trimmomatic
SUBDIR+=	vsearch
SUBDIR+=	xylem

.include "../mk/misc/category.mk"
py-biopython: initial commit The Biopython package contains high-quality, reusable modules and scripts written in Python to make it as easy as possible to use Python for bioinformatics. The Biopython includes the follwing: the ability to parse bioinformatics files into python utilizable data structures, including support for the formats such as Blast output, Clustalw, FASTA, GenBank, PubMed and Medicine, various Expasy files, SCOP, Rebase, UniGene, and SwissProt. 2019-08-09 23:52:34 +02:00			`# $NetBSD: Makefile,v 1.55 2019/08/09 21:52:34 brook Exp $`
Add new category biology 1999-04-16 01:17:30 +02:00			`#`

Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT. While I'm here, unify category Makefiles to more standard style. (If you have tools depending on the previous form, please fix them.) 2001-02-16 16:51:46 +01:00			`COMMENT= Software for the biological sciences`

Add and enable arka. 2005-03-27 15:09:19 +02:00			`SUBDIR+= arka`
Add azara. 2005-11-05 02:49:34 +01:00			`SUBDIR+= azara`
bcftools: added version 1.9 BCFtools is a program for variant calling and manipulating files 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. In order to avoid tedious repetion, throughout this document we will use "VCF" and "BCF" interchangeably, unless specifically noted. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF work in all situations. Unindexed VCF and BCF and streams work in most, but not all situations. In general, whenever multiple VCFs are read simultaneously, they must be indexed and therefore also compressed. 2018-11-15 10:21:24 +01:00			`SUBDIR+= bcftools`
Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT. While I'm here, unify category Makefiles to more standard style. (If you have tools depending on the previous form, please fix them.) 2001-02-16 16:51:46 +01:00			`SUBDIR+= bioperl`
Add bodr, chemical-mime-data, gnome-chemistry-utils, and openbabel. 2011-10-06 00:29:44 +02:00			`SUBDIR+= bodr`
Add bwa. 2015-10-14 19:13:44 +02:00			`SUBDIR+= bwa`
Add canu 2019-01-07 03:34:21 +01:00			`SUBDIR+= canu`
Add cdhit. 2015-10-12 18:49:03 +02:00			`SUBDIR+= cdhit`
Add bodr, chemical-mime-data, gnome-chemistry-utils, and openbabel. 2011-10-06 00:29:44 +02:00			`SUBDIR+= chemical-mime-data`
Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT. While I'm here, unify category Makefiles to more standard style. (If you have tools depending on the previous form, please fix them.) 2001-02-16 16:51:46 +01:00			`SUBDIR+= chemtool`
			`SUBDIR+= clustalw`
Add/enable coalesce. 2003-09-30 03:04:39 +02:00			`SUBDIR+= coalesce`
Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT. While I'm here, unify category Makefiles to more standard style. (If you have tools depending on the previous form, please fix them.) 2001-02-16 16:51:46 +01:00			`SUBDIR+= fastDNAml`
Add fastp 2019-05-04 18:16:10 +02:00			`SUBDIR+= fastp`
Add/enable fluctuate. 2003-09-30 03:20:02 +02:00			`SUBDIR+= fluctuate`
+ gabedit 2015-07-22 21:49:07 +02:00			`SUBDIR+= gabedit`
Add/enable genesplicer. 2003-09-30 03:57:35 +02:00			`SUBDIR+= genesplicer`
Add/enable glimmer. 2003-09-30 04:11:32 +02:00			`SUBDIR+= glimmer`
Add bodr, chemical-mime-data, gnome-chemistry-utils, and openbabel. 2011-10-06 00:29:44 +02:00			`SUBDIR+= gnome-chemistry-utils`
Add/enable gp. 2003-09-26 05:30:26 +02:00			`SUBDIR+= gp`
Sort list. 2010-03-18 09:02:32 +01:00			`SUBDIR+= gromacs`
Add hisat2 2019-01-15 02:27:42 +01:00			`SUBDIR+= hisat2`
Add/enable hmmer. 2003-09-26 05:53:10 +02:00			`SUBDIR+= hmmer`
Add htslib 2018-04-30 18:53:07 +02:00			`SUBDIR+= htslib`
Add kallisto 2018-12-21 20:03:46 +01:00			`SUBDIR+= kallisto`
Add and enable lucy. 2005-03-26 18:06:50 +01:00			`SUBDIR+= lucy`
Add misc/dvtm, biology/mopac, emulators/yabause. 2008-03-09 19:28:54 +01:00			`SUBDIR+= mopac`
+ mpqc 2013-03-16 13:45:33 +01:00			`SUBDIR+= mpqc`
Add/enable mummer 2003-09-28 00:25:54 +02:00			`SUBDIR+= mummer`
Add ncbi-blast+ 2018-04-27 22:30:24 +02:00			`SUBDIR+= ncbi-blast+`
Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT. While I'm here, unify category Makefiles to more standard style. (If you have tools depending on the previous form, please fix them.) 2001-02-16 16:51:46 +01:00			`SUBDIR+= nut`
Add bodr, chemical-mime-data, gnome-chemistry-utils, and openbabel. 2011-10-06 00:29:44 +02:00			`SUBDIR+= openbabel`
Add p5-Bio-ASN1-EntrezGene 2014-02-20 12:44:51 +01:00			`SUBDIR+= p5-Bio-ASN1-EntrezGene`
Add/enable pdbalign. 2003-09-26 05:18:15 +02:00			`SUBDIR+= pdbalign`
Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT. While I'm here, unify category Makefiles to more standard style. (If you have tools depending on the previous form, please fix them.) 2001-02-16 16:51:46 +01:00			`SUBDIR+= phylip`
+ plink 2012-09-14 19:49:03 +02:00			`SUBDIR+= plink`
+ plinkseq 2012-11-01 05:08:03 +01:00			`SUBDIR+= plinkseq`
Initial import of primer3. Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers. 2011-10-31 22:25:57 +01:00			`SUBDIR+= primer3`
Add/enable profit 2003-09-28 01:18:55 +02:00			`SUBDIR+= profit`
Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT. While I'm here, unify category Makefiles to more standard style. (If you have tools depending on the previous form, please fix them.) 2001-02-16 16:51:46 +01:00			`SUBDIR+= puzzle`
py-biopython: initial commit The Biopython package contains high-quality, reusable modules and scripts written in Python to make it as easy as possible to use Python for bioinformatics. The Biopython includes the follwing: the ability to parse bioinformatics files into python utilizable data structures, including support for the formats such as Blast output, Clustalw, FASTA, GenBank, PubMed and Medicine, various Expasy files, SCOP, Rebase, UniGene, and SwissProt. 2019-08-09 23:52:34 +02:00			`SUBDIR+= py-biopython`
Finish move of pymol to py-mol. 2007-08-12 05:21:06 +02:00			`SUBDIR+= py-mol`
biology: +py-pydicom 2018-10-31 21:16:30 +01:00			`SUBDIR+= py-pydicom`
Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT. While I'm here, unify category Makefiles to more standard style. (If you have tools depending on the previous form, please fix them.) 2001-02-16 16:51:46 +01:00			`SUBDIR+= rasmol`
Add samtools 2018-05-07 20:40:10 +02:00			`SUBDIR+= samtools`
Add/enable sewer 2003-09-28 01:36:59 +02:00			`SUBDIR+= sewer`
Add stacks 2018-12-22 22:53:23 +01:00			`SUBDIR+= stacks`
Add/enable stride 2003-09-28 01:47:20 +02:00			`SUBDIR+= stride`
Add trimmomatic 2018-07-25 17:15:50 +02:00			`SUBDIR+= trimmomatic`
Add vsearch 2019-05-10 18:20:22 +02:00			`SUBDIR+= vsearch`
Add/enable xylem 2003-10-04 21:16:29 +02:00			`SUBDIR+= xylem`
Add new category biology 1999-04-16 01:17:30 +02:00
Added mk/misc/category.mk, which contains the definitions that are only useful for category Makefiles, as opposed to bsd.pkg.subdir.mk, which is also relevant for the top-level directory. Adjusted the category Makefiles. 2007-08-13 10:12:41 +02:00			`.include "../mk/misc/category.mk"`