blast2go: Import blast2go-2.3.5 as wip/blast2go

[Brook Milligan <brook%nmsu.edu@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Thu Apr 7 10:40:57 2022 -0600
Changeset:	5b802a62f80311c1f4346198883d562a4ea08265

Modified Files:
	Makefile
Added Files:
	blast2go/DESCR
	blast2go/Makefile
	blast2go/PLIST
	blast2go/distinfo
	blast2go/files/blast2go.sh

Log Message:
blast2go: Import blast2go-2.3.5 as wip/blast2go

The Blast2GO (B2G) Pipeline Version (B2G4Pipe) runs B2G without any
graphical interface. B2G is an GO annotation and functional analysis
systems based on sequence similarity (Blast). The program extracts GO
terms to each obtained blast hit by mapping to existent annotation
associations. An annotation rule finally assigns GO terms to the query
sequence. Additionally you can add domian/motif based GO term obtained
through InterProScan searches. If you provide a folder with these xml
files the application will parse the XML belonging to for each
sequence and adds/merges the deduced GO terms to the BLAST based
annotations, allways taking into account the GO Ture Path Rule.  By
the B2G Desktop Application (www.blast2go.org) annotation and
functional analysis can be visualized in graph form reconstructing the
GO relationships and colour-highlighting the most relevant areas.

The output files generated by B2G4Pipe are equivalent to the file
generated by the desktop application. The annotation file (.annot) is
a tab separated file containing the sequence names and gene ontology
IDs.  An additional row holds a sequence description. The B2G Project
File (.dat) is a proprietary format and can be opened with the B2G
desktop application to perform manual re-annotations or GO base
analysis (Graph-Visualization, Fisher 2X2, statistic, bar/pies
charts). The ".dat" generation is not recomended when working with
very large datasets due to memory limitations.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=5b802a62f80311c1f4346198883d562a4ea08265

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

diffstat:
 Makefile                   |  1 +
 blast2go/DESCR             | 23 +++++++++++++++++++++++
 blast2go/Makefile          | 35 +++++++++++++++++++++++++++++++++++
 blast2go/PLIST             | 38 ++++++++++++++++++++++++++++++++++++++
 blast2go/distinfo          |  5 +++++
 blast2go/files/blast2go.sh |  7 +++++++
 6 files changed, 109 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index f44dde0e7b..a013d2c2e1 100644
--- a/Makefile
+++ b/Makefile
@@ -293,6 +293,7 @@ SUBDIR+=	bkchem
 SUBDIR+=	blad
 SUBDIR+=	blasr
 SUBDIR+=	blasr_libcpp
+SUBDIR+=	blast2go
 SUBDIR+=	bleachbit
 SUBDIR+=	blink
 SUBDIR+=	blueproxy
diff --git a/blast2go/DESCR b/blast2go/DESCR
new file mode 100644
index 0000000000..17d6fe743f
--- /dev/null
+++ b/blast2go/DESCR
@@ -0,0 +1,23 @@
+The Blast2GO (B2G) Pipeline Version (B2G4Pipe) runs B2G without any
+graphical interface. B2G is an GO annotation and functional analysis
+systems based on sequence similarity (Blast). The program extracts GO
+terms to each obtained blast hit by mapping to existent annotation
+associations. An annotation rule finally assigns GO terms to the query
+sequence. Additionally you can add domian/motif based GO term obtained
+through InterProScan searches. If you provide a folder with these xml
+files the application will parse the XML belonging to for each
+sequence and adds/merges the deduced GO terms to the BLAST based
+annotations, allways taking into account the GO Ture Path Rule.  By
+the B2G Desktop Application (www.blast2go.org) annotation and
+functional analysis can be visualized in graph form reconstructing the
+GO relationships and colour-highlighting the most relevant areas.
+
+The output files generated by B2G4Pipe are equivalent to the file
+generated by the desktop application. The annotation file (.annot) is
+a tab separated file containing the sequence names and gene ontology
+IDs.  An additional row holds a sequence description. The B2G Project
+File (.dat) is a proprietary format and can be opened with the B2G
+desktop application to perform manual re-annotations or GO base
+analysis (Graph-Visualization, Fisher 2X2, statistic, bar/pies
+charts). The ".dat" generation is not recomended when working with
+very large datasets due to memory limitations.
diff --git a/blast2go/Makefile b/blast2go/Makefile
new file mode 100644
index 0000000000..d1b5bb1bc9
--- /dev/null
+++ b/blast2go/Makefile
@@ -0,0 +1,35 @@
+# $NetBSD$
+
+DISTNAME=	b2g4pipe235
+PKGNAME=	blast2go-2.3.5
+CATEGORIES=	biology
+MASTER_SITES=	https://www.blast2go.org/_media/
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://www.blast2go.org/
+COMMENT=	GO annotation and functional genome analysis
+#LICENSE=	# TODO: (see mk/license.mk)
+
+WRKSRC=		${WRKDIR}/b2g4pipe
+USE_JAVA=	run
+USE_TOOLS+=	pax
+NO_BUILD=	yes
+
+SUBST_CLASSES+=		java
+SUBST_STAGE.java=	pre-configure
+SUBST_FILES.java=	blast2go.sh
+SUBST_VARS.java=	PREFIX JAVA_BINPREFIX
+
+INSTALLATION_DIRS+=	bin libexec/blast2go share/doc/blast2go share/examples/blast2go
+
+post-extract:
+	${CP} ${FILESDIR}/blast2go.sh ${WRKSRC}
+
+do-install:
+	${INSTALL_SCRIPT} ${WRKSRC}/blast2go.sh ${DESTDIR}${PREFIX}/bin/blast2go
+	cd ${WRKSRC} && ${PAX} -rw blast2go.jar ext ${DESTDIR}${PREFIX}/libexec/blast2go
+	${INSTALL_DATA} ${WRKSRC}/b2gpipe_readme_v2_3_5.txt ${DESTDIR}${PREFIX}/share/doc/blast2go
+	${INSTALL_DATA} ${WRKSRC}/b2gPipe.properties ${DESTDIR}${PREFIX}/share/examples/blast2go
+
+.include "../../mk/java-vm.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/blast2go/PLIST b/blast2go/PLIST
new file mode 100644
index 0000000000..827a8d6370
--- /dev/null
+++ b/blast2go/PLIST
@@ -0,0 +1,38 @@
+@comment $NetBSD$
+bin/blast2go
+libexec/blast2go/blast2go.jar
+libexec/blast2go/ext/axis/axis-ant.jar
+libexec/blast2go/ext/axis/axis.jar
+libexec/blast2go/ext/axis/axisall.jar
+libexec/blast2go/ext/axis/commons-discovery-0.2.jar
+libexec/blast2go/ext/axis/commons-logging-1.0.4.jar
+libexec/blast2go/ext/axis/jaxrpc.jar
+libexec/blast2go/ext/axis/keggapi.jar
+libexec/blast2go/ext/axis/log4j-1.2.8.jar
+libexec/blast2go/ext/axis/saaj.jar
+libexec/blast2go/ext/axis/wsdl4j-1.5.1.jar
+libexec/blast2go/ext/biojava-1.3.1.jar
+libexec/blast2go/ext/ext.jar
+libexec/blast2go/ext/interpro/commons-cli-1.0.jar
+libexec/blast2go/ext/interpro/commons-cli.jar
+libexec/blast2go/ext/interpro/freefluo.jar
+libexec/blast2go/ext/interpro/interpro.jar
+libexec/blast2go/ext/interpro/servlet.jar
+libexec/blast2go/ext/jakarta-regexp-1.4.jar
+libexec/blast2go/ext/jcommon-1.0.0.jar
+libexec/blast2go/ext/jdom/activation.jar
+libexec/blast2go/ext/jdom/ant.jar
+libexec/blast2go/ext/jdom/jaxen-core.jar
+libexec/blast2go/ext/jdom/jaxen-jdom.jar
+libexec/blast2go/ext/jdom/jdom.jar
+libexec/blast2go/ext/jdom/jdomall.jar
+libexec/blast2go/ext/jdom/mail.jar
+libexec/blast2go/ext/jdom/saxpath.jar
+libexec/blast2go/ext/jdom/xalan.jar
+libexec/blast2go/ext/jdom/xerces.jar
+libexec/blast2go/ext/jdom/xml-apis.jar
+libexec/blast2go/ext/jfreechart-1.0.1.jar
+libexec/blast2go/ext/mysql-connector-java-3.0.11-stable-bin.jar
+libexec/blast2go/ext/zvtm.jar
+share/doc/blast2go/b2gpipe_readme_v2_3_5.txt
+share/examples/blast2go/b2gPipe.properties
diff --git a/blast2go/distinfo b/blast2go/distinfo
new file mode 100644
index 0000000000..a30ab10248
--- /dev/null
+++ b/blast2go/distinfo
@@ -0,0 +1,5 @@
+$NetBSD$
+
+BLAKE2s (b2g4pipe235.tar.gz) = 1976628fcae76385403eacf80e5cf8dc7a4e43a7172f1fee9ae59ead4cc14713
+SHA512 (b2g4pipe235.tar.gz) = e985d63273704b340074355d54d08b9326665d59aabc74076207f42c214211df8ba95697ecb25ccdd2fe03b3e16b7f13f1d8066cc16e58dc906c799ec3faa29c
+Size (b2g4pipe235.tar.gz) = 11907278 bytes
diff --git a/blast2go/files/blast2go.sh b/blast2go/files/blast2go.sh
new file mode 100644
index 0000000000..cefd5e4784
--- /dev/null
+++ b/blast2go/files/blast2go.sh
@@ -0,0 +1,7 @@
+#!/bin/sh
+# blast2go.sh
+
+JAVA=@JAVA_BINPREFIX@-java
+JAR=@PREFIX@/libexec/blast2go/blast2go.jar
+
+exec ${JAVA} -jar ${JAR} ${*}