pkgsrc/biology/Makefile

# $NetBSD: Makefile,v 1.98 2023/11/05 17:59:52 bacon Exp $
#

COMMENT=	Software for the biological sciences

SUBDIR+=	R-popbio
SUBDIR+=	ad2vcf
SUBDIR+=	arka
SUBDIR+=	atac-seq
SUBDIR+=	azara
SUBDIR+=	balance-tui
SUBDIR+=	bcftools
SUBDIR+=	beagle
SUBDIR+=	bedtools
SUBDIR+=	biolibc
SUBDIR+=	biolibc-tools
SUBDIR+=	bioperl
SUBDIR+=	bodr
SUBDIR+=	bowtie2
SUBDIR+=	bwa
SUBDIR+=	canu
SUBDIR+=	cdhit
SUBDIR+=	chemtool
SUBDIR+=	chip-seq
SUBDIR+=	clustalw
SUBDIR+=	coalesce
SUBDIR+=	coordgenlibs
SUBDIR+=	fasda
SUBDIR+=	fastDNAml
SUBDIR+=	fastp
SUBDIR+=	fastq-trim
SUBDIR+=	fastqc
SUBDIR+=	fastx-toolkit
SUBDIR+=	filter-fastq
SUBDIR+=	fluctuate
SUBDIR+=	gabedit
SUBDIR+=	generand
SUBDIR+=	genesplicer
SUBDIR+=	gffread
SUBDIR+=	glimmer
SUBDIR+=	gp
SUBDIR+=	gromacs
SUBDIR+=	hisat2
SUBDIR+=	hmmer
SUBDIR+=	htslib
SUBDIR+=	igv
SUBDIR+=	kallisto
SUBDIR+=	lucy
SUBDIR+=	maeparser
SUBDIR+=	microsynteny-tools
SUBDIR+=	miniasm
SUBDIR+=	minimap2
SUBDIR+=	molsketch
SUBDIR+=	mopac
SUBDIR+=	mpqc
SUBDIR+=	mummer
SUBDIR+=	ncbi-blast+
SUBDIR+=	nut
SUBDIR+=	openbabel
SUBDIR+=	p5-Bio-ASN1-EntrezGene
SUBDIR+=	pdbalign
SUBDIR+=	peak-classifier
SUBDIR+=	phylip
SUBDIR+=	plink
SUBDIR+=	plinkseq
SUBDIR+=	primer3
SUBDIR+=	profit
SUBDIR+=	puzzle
SUBDIR+=	py-bcbio-gff
SUBDIR+=	py-biopython
SUBDIR+=	py-cutadapt
SUBDIR+=	py-dna-features-viewer
SUBDIR+=	py-dnaio
SUBDIR+=	py-macs2
SUBDIR+=	py-multiqc
SUBDIR+=	py-pydicom
SUBDIR+=	racon
SUBDIR+=	rasmol
SUBDIR+=	rna-seq
SUBDIR+=	rna-star
SUBDIR+=	samtools
SUBDIR+=	seqtk
SUBDIR+=	sewer
SUBDIR+=	sra-tools
SUBDIR+=	stacks
SUBDIR+=	stride
SUBDIR+=	stringtie
SUBDIR+=	trimmomatic
SUBDIR+=	vcf-split
SUBDIR+=	vcf2hap
SUBDIR+=	vsearch
SUBDIR+=	xmakemol
SUBDIR+=	xylem

.include "../mk/misc/category.mk"
biology/Makefile: Add microsynteny tools 2023-11-05 18:59:52 +01:00			`# $NetBSD: Makefile,v 1.98 2023/11/05 17:59:52 bacon 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`

biology/R-popbio: import R-popbio-2.7 Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002). 2020-08-10 20:18:46 +02:00			`SUBDIR+= R-popbio`
biology/Makefile: Add ad2vcf 2021-03-24 19:20:39 +01:00			`SUBDIR+= ad2vcf`
Add and enable arka. 2005-03-27 15:09:19 +02:00			`SUBDIR+= arka`
biology/Makefile: Add atac-seq 2023-01-23 22:39:11 +01:00			`SUBDIR+= atac-seq`
Add azara. 2005-11-05 02:49:34 +01:00			`SUBDIR+= azara`
Add balance-tui 2022-11-28 10:54:00 +01:00			`SUBDIR+= balance-tui`
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`
Added biology/beagle version 5.2 2021-05-26 21:14:24 +02:00			`SUBDIR+= beagle`
biology/Makefile: Add bedtools 2021-01-22 18:09:00 +01:00			`SUBDIR+= bedtools`
biology/Makefile: Add biolibc, vcf-split 2021-03-24 16:24:55 +01:00			`SUBDIR+= biolibc`
biology/Makefile: Add biolibc-tools 2021-08-31 17:56:42 +02:00			`SUBDIR+= biolibc-tools`
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`
biology/Makefile: Add bowtie2 2021-01-21 18:30:59 +01:00			`SUBDIR+= bowtie2`
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`
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`
biology/Makefile: Add chip-seq 2023-06-14 23:28:54 +02:00			`SUBDIR+= chip-seq`
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+= clustalw`
Add/enable coalesce. 2003-09-30 03:04:39 +02:00			`SUBDIR+= coalesce`
New package, coordgenlibs-1.4.2. Part of PR pkg/55755. This is Schroedinger, Inc's 2D coordinate generation. It was formerly proprietary code, but is now released under the BSD license. The emphasis of these algorithms are on quality of 2D coordinates rather than speed of generation. The algorithm distinguishes itself from many others by doing well with both macrocycles and metal complexes. It also does extremely well on typical drug-like small molecules, and has been validated on millions of compounds. 2020-11-03 21:17:59 +01:00			`SUBDIR+= coordgenlibs`
biology/Makefile: Add fasda 2022-12-12 19:29:06 +01:00			`SUBDIR+= fasda`
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`
biology/Makefile: Add fastq-trim 2022-11-06 23:50:02 +01:00			`SUBDIR+= fastq-trim`
biology/Makefile: Add fastqc 2021-01-20 16:57:49 +01:00			`SUBDIR+= fastqc`
biology/Makefile: Add fastx-toolkit 2022-04-05 20:49:29 +02:00			`SUBDIR+= fastx-toolkit`
biology/filter-fastq: add filter-fastq version 0.0.0.20210527 2021-05-27 19:13:15 +02:00			`SUBDIR+= filter-fastq`
Add/enable fluctuate. 2003-09-30 03:20:02 +02:00			`SUBDIR+= fluctuate`
+ gabedit 2015-07-22 21:49:07 +02:00			`SUBDIR+= gabedit`
biology/Makefile: Add generand 2021-03-21 15:24:39 +01:00			`SUBDIR+= generand`
Add/enable genesplicer. 2003-09-30 03:57:35 +02:00			`SUBDIR+= genesplicer`
biology/Makefile: Add gffread 2022-11-07 00:01:44 +01:00			`SUBDIR+= gffread`
Add/enable glimmer. 2003-09-30 04:11:32 +02:00			`SUBDIR+= glimmer`
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`
biology/Makefile: + igv 2021-02-24 15:05:25 +01:00			`SUBDIR+= igv`
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`
New package, maeparser-1.4.2. maeparser is a parser for Schrodinger Maestro files. Structure files (.mae,.maegz,.mae.gz) can contain multiple structures delimited by "f_m_ct". See MaeConstants.hpp for standard block and property names. 2020-11-03 17:41:26 +01:00			`SUBDIR+= maeparser`
biology/Makefile: Add microsynteny tools 2023-11-05 18:59:52 +01:00			`SUBDIR+= microsynteny-tools`
Add biology/miniasm 0.3. 2021-05-26 20:46:41 +02:00			`SUBDIR+= miniasm`
Add biology/minimap2 2.18 2021-05-26 20:51:07 +02:00			`SUBDIR+= minimap2`
Add biology/molsketch 2020-12-18 23:30:28 +01:00			`SUBDIR+= molsketch`
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`
biology/Makefile: Add peak-classifier 2021-06-15 15:55:35 +02:00			`SUBDIR+= peak-classifier`
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`
biology/Makefile: Add py-bcbio-gff 2023-11-05 18:52:08 +01:00			`SUBDIR+= py-bcbio-gff`
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`
biology/Makefile: sort entries 2021-02-12 01:24:35 +01:00			`SUBDIR+= py-cutadapt`
biology/Makefile: Add py-dna-features-viewer 2023-11-05 18:55:08 +01:00			`SUBDIR+= py-dna-features-viewer`
biology/Makefile: sort entries 2021-02-12 01:24:35 +01:00			`SUBDIR+= py-dnaio`
biology/Makefile: Add py-macs2 2023-01-23 00:30:51 +01:00			`SUBDIR+= py-macs2`
biology/Makefile: Add py-multiqc 2023-07-22 15:19:17 +02:00			`SUBDIR+= py-multiqc`
biology: +py-pydicom 2018-10-31 21:16:30 +01:00			`SUBDIR+= py-pydicom`
Added biology/racon 1.4.3 2021-05-26 20:54:29 +02:00			`SUBDIR+= racon`
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`
biology/Makefile: Add rna-seq meta-package 2022-12-12 19:40:02 +01:00			`SUBDIR+= rna-seq`
biology/Makefile: Add rna-star 2023-07-31 16:34:52 +02:00			`SUBDIR+= rna-star`
Add samtools 2018-05-07 20:40:10 +02:00			`SUBDIR+= samtools`
biology/Makefile: Add seqtk 2023-05-24 01:19:57 +02:00			`SUBDIR+= seqtk`
Add/enable sewer 2003-09-28 01:36:59 +02:00			`SUBDIR+= sewer`
biology/Makefile: Add sra-tools 2023-08-29 02:00:48 +02:00			`SUBDIR+= sra-tools`
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`
biology/Makefile: Add stringtie 2023-08-12 16:58:55 +02:00			`SUBDIR+= stringtie`
Add trimmomatic 2018-07-25 17:15:50 +02:00			`SUBDIR+= trimmomatic`
biology/Makefile: Add biolibc, vcf-split 2021-03-24 16:24:55 +01:00			`SUBDIR+= vcf-split`
biology/Makefile: Add vcf2hap 2021-03-24 19:23:33 +01:00			`SUBDIR+= vcf2hap`
Add vsearch 2019-05-10 18:20:22 +02:00			`SUBDIR+= vsearch`
+ xmakemol 2022-12-30 19:19:02 +01:00			`SUBDIR+= xmakemol`
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"`