biostar-tools: Meta-package for Biostar Handbook tools

[Jason W. Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu Feb 15 10:17:25 2024 -0600
Changeset:	1abce1bb10642286f3d727f5e9e7494f7cc4eba6

Modified Files:
	Makefile
Added Files:
	biostar-tools/DESCR
	biostar-tools/Makefile
	biostar-tools/files/biostar-shell.in

Log Message:
biostar-tools: Meta-package for Biostar Handbook tools

Biostar-Tools is a metaport for installing all the tools necessary to work
through the Biostar Handbook, except for bedGrapToBigWig, which has license
restrictions.  If you need bedGraphToBigWig, run

	cd /usr/pkgsrc/biology/ucsc-userapps && make install clean

The handbook instructs the user to install these tools mostly via bioconda,
which then requires the user to activate the bioconda environment each time
they want to use the tools.  This meta-package installs all of the tools
except emboss to the default PATH so they just work without any special
environment.  Emboss commands are installed to /usr/pkg/emboss/bin due to
conflicts with other packages.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=1abce1bb10642286f3d727f5e9e7494f7cc4eba6

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

diffstat:
 Makefile                             |  1 +
 biostar-tools/DESCR                  | 12 +++++
 biostar-tools/Makefile               | 93 ++++++++++++++++++++++++++++++++++++
 biostar-tools/files/biostar-shell.in | 29 +++++++++++
 4 files changed, 135 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 489c57f162..bae6ccaa87 100644
--- a/Makefile
+++ b/Makefile
@@ -287,6 +287,7 @@ SUBDIR+=	bio-mocha
 SUBDIR+=	biolibc
 SUBDIR+=	biolibc-tools
 SUBDIR+=	bioruby
+SUBDIR+=	biostar-tools
 SUBDIR+=	bip
 SUBDIR+=	bitkeeper
 SUBDIR+=	bitlbee-purple
diff --git a/biostar-tools/DESCR b/biostar-tools/DESCR
new file mode 100644
index 0000000000..a3b9cac83d
--- /dev/null
+++ b/biostar-tools/DESCR
@@ -0,0 +1,12 @@
+Biostar-Tools is a metaport for installing all the tools necessary to work
+through the Biostar Handbook, except for bedGrapToBigWig, which has license
+restrictions.  If you need bedGraphToBigWig, run
+
+	cd /usr/pkgsrc/biology/ucsc-userapps && make install clean
+
+The handbook instructs the user to install these tools mostly via bioconda,
+which then requires the user to activate the bioconda environment each time
+they want to use the tools.  This meta-package installs all of the tools
+except emboss to the default PATH so they just work without any special
+environment.  Emboss commands are installed to /usr/pkg/emboss/bin due to
+conflicts with other packages.
diff --git a/biostar-tools/Makefile b/biostar-tools/Makefile
new file mode 100644
index 0000000000..f8c4748f8e
--- /dev/null
+++ b/biostar-tools/Makefile
@@ -0,0 +1,93 @@
+# $NetBSD$
+#
+
+DISTNAME=	biostar-tools
+CATEGORIES=	biology meta-pkgs
+MASTER_SITES=	# empty
+
+OWNER=		bacon%NetBSD.org@localhost
+COMMENT=	Meta-package for Biostar Handbook tools
+
+WWW=            https://www.biostarhandbook.com
+
+LICENSE=        BSD2CLAUSE
+
+# For a current list see http://data.biostarhandbook.com/install/conda.txt.
+# Also included are some programs not listed above, but mentioned in the text.
+# TODO: Add hdfview
+
+DEPENDS+=	fastq-trim>0:../../wip/fastq-trim
+DEPENDS+=	fastqc>0:../../biology/fastqc
+DEPENDS+=	biolibc-tools>0:../../wip/biolibc-tools
+DEPENDS+=	gffread>0:../../biology/gffread
+DEPENDS+=	kallisto>0:../../biology/kallisto
+DEPENDS+=	hisat2>0:../../biology/hisat2
+DEPENDS+=	samtools>0:../../biology/samtools
+DEPENDS+=	igv>0:../../biology/igv
+DEPENDS+=	${PYPKGPREFIX}-multiqc-[0-9]*:../../wip/py-multiqc
+DEPENDS+=	wget>0:../../net/wget
+DEPENDS+=	curl>0:../../www/curl
+DEPENDS+=	lz4>0:../../archivers/lz4
+DEPENDS+=	xz>0:../../archivers/xz
+DEPENDS+=	zstd>0:../../archivers/zstd
+
+# Allow pkg build on non-amd64 systems until sra-tools supports them
+.if ${MACHINE_ARCH} == amd64 || ${MACHINE_ARCH} == aarch64
+DEPENDS+=   sra-tools>0:biology/sra-tools
+.endif
+
+META_PACKAGE=	yes
+
+# FreeBSD port depends:
+#                 nano>0:editors/nano \
+#                 parallel>0:sysutils/parallel \
+#                 seqkit>0:biology/seqkit \
+#                 csvtk>0:science/csvtk \
+#                 ${PYTHON_PKGNAMEPREFIX}csvkit>0:textproc/py-csvkit@${PY_FLAVOR} \
+#                 miller>0:textproc/miller \
+#                 ncbi-entrez-direct>0:biology/ncbi-entrez-direct \
+#                 readseq>0:biology/readseq \
+#                 snpeff>0:biology/snpeff \
+#                 picard-tools>0:biology/picard-tools \
+#                 bbmap>0:biology/bbmap \
+#                 minimap2>0:biology/minimap2 \
+#                 bwa>0:biology/bwa \
+#                 bowtie2>0:biology/bowtie2 \
+#                 emboss>0:biology/emboss \
+#                 bedtools>0:biology/bedtools \
+#                 bamtools>0:biology/bamtools \
+#                 ${PYTHON_PKGNAMEPREFIX}cutadapt>0:biology/py-cutadapt@${PY_FLAVOR} \
+#                 seqtk>0:biology/seqtk \
+#                 datamash>0:textproc/datamash \
+#                 bcftools>0:biology/bcftools \
+#                 subread>0:biology/subread \
+#                 trimmomatic>0:biology/trimmomatic \
+#                 picard-tools>0:biology/picard-tools \
+#                 ncbi-blast+>0:biology/ncbi-blast+ \
+#                 cd-hit>0:biology/cd-hit \
+#                 ${PYTHON_PKGNAMEPREFIX}biopython>0:biology/py-biopython@${PY_FLAVOR} \
+#                 ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR} \
+#                 freebayes>0:biology/freebayes \
+#                 p5-Net-SSLeay>0:security/p5-Net-SSLeay \
+#                 bioawk>0:biology/bioawk \
+#                 vt>0:biology/vt \
+#                 ${PYTHON_PKGNAMEPREFIX}crossmap>0:biology/py-crossmap@${PY_FLAVOR} \
+#                 ${PYTHON_PKGNAMEPREFIX}goatools>0:biology/py-goatools@${PY_FLAVOR} \
+#                 erminej>0:biology/erminej \
+#                 ${PYTHON_PKGNAMEPREFIX}ont-fast5-api>0:biology/py-ont-fast5-api@${PY_FLAVOR} \
+#                 flash>0:biology/flash \
+#                 bfc:biology/bfc \
+#                 Jellyfish>0:biology/jellyfish \
+#                 mafft>0:biology/mafft \
+#                 clustal-omega>0:biology/clustal-omega \
+#                 ${PYTHON_PKGNAMEPREFIX}pywgsim>0:biology/py-pywgsim@${PY_FLAVOR} \
+#                 sam2pairwise>0:biology/sam2pairwise \
+#                 bamutil>0:biology/bamutil \
+#                 ${PYTHON_PKGNAMEPREFIX}deepTools>0:biology/py-deeptools@${PY_FLAVOR} \
+
+# do-install:
+# 	@${MKDIR} ${STAGEDIR}${PREFIX}/bin
+# 	${INSTALL_SCRIPT} ${WRKDIR}/biostar-shell ${STAGEDIR}${PREFIX}/bin
+
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/biostar-tools/files/biostar-shell.in b/biostar-tools/files/biostar-shell.in
new file mode 100755
index 0000000000..275572a3b6
--- /dev/null
+++ b/biostar-tools/files/biostar-shell.in
@@ -0,0 +1,29 @@
+#!/bin/sh -e
+
+ucsc_bin=%%PREFIX%%/userapps/bin
+emboss_bin=%%PREFIX%%/emboss/bin
+cat << EOM
+
+Adding $ucsc_bin and $emboss_bin to \$PATH.
+
+UCSC kent utils and emboss contain commands that conflict with other tools,
+including at least "calc", "mktime", and "stringify".
+
+The other commands with these names may serve entirely different functions
+and will not be accessible while running this shell unless you refer to them
+by their absolute path name (e.g. /usr/local/bin/calc), which is not portable,
+BTW, so don't hard-code such paths into your scripts.
+
+Type "exit" or "Ctrl+D" to return to your normal shell.
+
+EOM
+
+export PATH=${ucsc_bin}:${emboss_bin}:$PATH
+
+# FIXME: Update shell prompts to include (ucsc-kent)?
+
+# Invoke the user's chosen shell
+if echo $SHELL | egrep -q '/t?csh'; then
+    args='-f'
+fi
+exec $SHELL $args