repeatmasker: Import repeatmasker-4.1.2-p1 as wip/repeatmasker.

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: repeatmasker: Import repeatmasker-4.1.2-p1 as wip/repeatmasker.
From: Brook Milligan <brook%nmsu.edu@localhost>
Date: Mon, 13 Sep 2021 19:48:22 +0000
Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Mon Sep 13 13:48:22 2021 -0600
Changeset:	7389ab32a6265ed4f99e14367eccec8f1660995b

Modified Files:
	Makefile
Added Files:
	repeatmasker/DESCR
	repeatmasker/Makefile
	repeatmasker/PLIST
	repeatmasker/distinfo
	repeatmasker/patches/patch-configure

Log Message:
repeatmasker: Import repeatmasker-4.1.2-p1 as wip/repeatmasker.

RepeatMasker is a program that screens DNA sequences for interspersed
repeats and low complexity DNA sequences. The output of the program is
a detailed annotation of the repeats that are present in the query
sequence as well as a modified version of the query sequence in which
all the annotated repeats have been masked (default: replaced by
Ns). Sequence comparisons in RepeatMasker are performed by the program
cross_match, an efficient implementation of the Smith-Waterman-Gotoh
algorithm developed by Phil Green, or by WU-Blast developed by Warren
Gish.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=7389ab32a6265ed4f99e14367eccec8f1660995b

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

diffstat:
 Makefile                             |   1 +
 repeatmasker/DESCR                   |   9 ++
 repeatmasker/Makefile                |  83 ++++++++++++++
 repeatmasker/PLIST                   | 213 +++++++++++++++++++++++++++++++++++
 repeatmasker/distinfo                |   7 ++
 repeatmasker/patches/patch-configure |  24 ++++
 6 files changed, 337 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 168a61c305..b3e1c4b1b1 100644
--- a/Makefile
+++ b/Makefile
@@ -4951,6 +4951,7 @@ SUBDIR+=	regexxer
 SUBDIR+=	relaydb
 SUBDIR+=	remctl
 SUBDIR+=	reone
+SUBDIR+=	repeatmasker
 SUBDIR+=	reproc
 SUBDIR+=	resid-builder
 SUBDIR+=	residualvm
diff --git a/repeatmasker/DESCR b/repeatmasker/DESCR
new file mode 100644
index 0000000000..741522d08b
--- /dev/null
+++ b/repeatmasker/DESCR
@@ -0,0 +1,9 @@
+RepeatMasker is a program that screens DNA sequences for interspersed
+repeats and low complexity DNA sequences. The output of the program is
+a detailed annotation of the repeats that are present in the query
+sequence as well as a modified version of the query sequence in which
+all the annotated repeats have been masked (default: replaced by
+Ns). Sequence comparisons in RepeatMasker are performed by the program
+cross_match, an efficient implementation of the Smith-Waterman-Gotoh
+algorithm developed by Phil Green, or by WU-Blast developed by Warren
+Gish.
diff --git a/repeatmasker/Makefile b/repeatmasker/Makefile
new file mode 100644
index 0000000000..3aa1a07614
--- /dev/null
+++ b/repeatmasker/Makefile
@@ -0,0 +1,83 @@
+# $NetBSD$
+
+DISTNAME=	RepeatMasker-4.1.2-p1
+PKGNAME=	repeatmasker-4.1.2.1
+CATEGORIES=	biology
+MASTER_SITES=	http://www.repeatmasker.org/RepeatMasker/
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	http://www.repeatmasker.org/RepeatMasker/
+COMMENT=	Find interspersed repeats and low complexity DNA sequences
+LICENSE=	osl # v2.1 but licenses/osl is v3.0
+
+WRKSRC=		${WRKDIR}/RepeatMasker
+HAS_CONFIGURE=	yes
+USE_LANGUAGES=	# none
+USE_TOOLS+=	pax perl
+NO_BUILD=	yes
+
+DEPENDS+=	${PYPKGPREFIX}-h5py>=2.9.0:../../devel/py-h5py
+DEPENDS+=	trf>=4.09.1:../../wip/trf
+
+# use options? crossmatch, rmblast, nhmmer, abblast/wublast
+# valid search engine values: ncbi|rmblast|wublast|abblast|crossmatch|hmmer|nhmmer
+CONFIGURE_ARGS+=	-default_search_engine=hmmer
+DEPENDS+=		hmmer>=3.1:../../wip/hmmer
+
+CONFIGURE_ARGS+=	-abblast_dir=${PREFIX}/bin
+CONFIGURE_ARGS+=	-crossmatch_dir=${PREFIX}/bin
+CONFIGURE_ARGS+=	-hmmer_dir=${PREFIX}/bin
+CONFIGURE_ARGS+=	-rmblast_dir=${PREFIX}/bin
+
+CONFIGURE_ARGS+=	-trf_prgm=${PREFIX}/bin/trf
+
+PYTHON_VERSIONS_INCOMPATIBLE=	27
+SUBST_CLASSES+=			python3
+SUBST_STAGE.python3=		pre-configure
+SUBST_FILES.python3=		configure
+SUBST_VARS.python3=		PYTHONBIN
+
+REPLACE_PERL+=		*.pm
+REPLACE_PERL+=		configure
+REPLACE_PERL+=		util/*.pl
+REPLACE_PERL+=		util/trfMask
+REPLACE_PYTHON+=	famdb.py
+REPLACE_PYTHON+=	util/RM2Bed.py
+
+# XXX - LIBDIR is used to find the location of files when installed
+# programs are run.  However, configure tests for distributed files in
+# ${LIBDIR} when it runs.  Thus, LIBDIR cannot point to a directory
+# first created during installation, so the default is used initially
+# then replaced prior to installation.
+#
+SUBST_CLASSES+=		LIBDIR
+SUBST_STAGE.LIBDIR=	pre-install
+SUBST_FILES.LIBDIR=	RepeatMaskerConfig.pm
+SUBST_SED.LIBDIR=	-e "s,'value' => '.*/RepeatMasker/Libraries','value' => '${PREFIX}/RepeatMasker/Libraries',"
+
+post-extract:
+	${CHMOD} a-x ${WRKSRC}/Libraries/Artefacts.embl
+	${CHMOD} a-x ${WRKSRC}/Libraries/RepeatAnnotationData.pm
+
+do-configure:
+	cd ${WRKSRC} && ${ENV} ${CONFIGURE_ENV} ${PERL5} configure ${CONFIGURE_ARGS}
+
+INSTALLATION_DIRS+=	RepeatMasker lib/RepeatMasker share/doc/RepeatMasker
+DOC_FILES+=		README.md daterepeats.help repeatmasker.help
+# XXX - easier to copy everything and delete a few files
+UNINSTALLED_FILES+=	.github INSTALL LICENSE ReleaseNotes configure.orig ${DOC_FILES}
+
+pre-install:
+	cd ${WRKSRC}/Libraries && ${LN} -sf Dfam.h5 RepeatMaskerLib.h5
+
+do-install:
+	cd ${WRKSRC} && ${PAX} -rw * ${DESTDIR}${PREFIX}/RepeatMasker
+	cd ${DESTDIR}${PREFIX}/RepeatMasker && ${RM} -rf ${UNINSTALLED_FILES}
+.for f in ${DOC_FILES}
+	${INSTALL_DATA} ${WRKSRC}/${f} ${DESTDIR}${PREFIX}/share/doc/RepeatMasker
+.endfor
+
+.include "../../lang/python/application.mk"
+.include "../../lang/python/pyversion.mk"
+.include "../../wip/ncbi-blast+/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/repeatmasker/PLIST b/repeatmasker/PLIST
new file mode 100644
index 0000000000..0157bda23c
--- /dev/null
+++ b/repeatmasker/PLIST
@@ -0,0 +1,213 @@
+@comment $NetBSD$
+RepeatMasker/ArrayList.pm
+RepeatMasker/ArrayListIterator.pm
+RepeatMasker/CrossmatchSearchEngine.pm
+RepeatMasker/DFAM.pm
+RepeatMasker/DFAMRecord.pm
+RepeatMasker/DateRepeats
+RepeatMasker/DupMasker
+RepeatMasker/EMBL.pm
+RepeatMasker/FastaDB.pm
+RepeatMasker/HMMERSearchEngine.pm
+RepeatMasker/HTMLAnnotHeader.html
+RepeatMasker/Libraries/Artefacts.embl
+RepeatMasker/Libraries/Dfam.h5
+RepeatMasker/Libraries/README.meta
+RepeatMasker/Libraries/RMRBMeta.embl
+RepeatMasker/Libraries/RepeatAnnotationData.pm
+RepeatMasker/Libraries/RepeatMasker.lib
+RepeatMasker/Libraries/RepeatMaskerLib.h5
+RepeatMasker/Libraries/RepeatPeps.lib
+RepeatMasker/Libraries/RepeatPeps.readme
+RepeatMasker/Libraries/taxonomy.dat
+RepeatMasker/LibraryUtils.pm
+RepeatMasker/Matrices/crossmatch/14p35g.matrix
+RepeatMasker/Matrices/crossmatch/14p37g.matrix
+RepeatMasker/Matrices/crossmatch/14p39g.matrix
+RepeatMasker/Matrices/crossmatch/14p41g.matrix
+RepeatMasker/Matrices/crossmatch/14p43g.matrix
+RepeatMasker/Matrices/crossmatch/14p45g.matrix
+RepeatMasker/Matrices/crossmatch/14p47g.matrix
+RepeatMasker/Matrices/crossmatch/14p49g.matrix
+RepeatMasker/Matrices/crossmatch/14p51g.matrix
+RepeatMasker/Matrices/crossmatch/14p53g.matrix
+RepeatMasker/Matrices/crossmatch/18p35g.matrix
+RepeatMasker/Matrices/crossmatch/18p37g.matrix
+RepeatMasker/Matrices/crossmatch/18p39g.matrix
+RepeatMasker/Matrices/crossmatch/18p41g.matrix
+RepeatMasker/Matrices/crossmatch/18p43g.matrix
+RepeatMasker/Matrices/crossmatch/18p45g.matrix
+RepeatMasker/Matrices/crossmatch/18p47g.matrix
+RepeatMasker/Matrices/crossmatch/18p49g.matrix
+RepeatMasker/Matrices/crossmatch/18p51g.matrix
+RepeatMasker/Matrices/crossmatch/18p53g.matrix
+RepeatMasker/Matrices/crossmatch/20p35g.matrix
+RepeatMasker/Matrices/crossmatch/20p37g.matrix
+RepeatMasker/Matrices/crossmatch/20p39g.matrix
+RepeatMasker/Matrices/crossmatch/20p41g.matrix
+RepeatMasker/Matrices/crossmatch/20p43g.matrix
+RepeatMasker/Matrices/crossmatch/20p45g.matrix
+RepeatMasker/Matrices/crossmatch/20p47g.matrix
+RepeatMasker/Matrices/crossmatch/20p49g.matrix
+RepeatMasker/Matrices/crossmatch/20p51g.matrix
+RepeatMasker/Matrices/crossmatch/20p53g.matrix
+RepeatMasker/Matrices/crossmatch/25p35g.matrix
+RepeatMasker/Matrices/crossmatch/25p37g.matrix
+RepeatMasker/Matrices/crossmatch/25p39g.matrix
+RepeatMasker/Matrices/crossmatch/25p41g.matrix
+RepeatMasker/Matrices/crossmatch/25p43g.matrix
+RepeatMasker/Matrices/crossmatch/25p45g.matrix
+RepeatMasker/Matrices/crossmatch/25p47g.matrix
+RepeatMasker/Matrices/crossmatch/25p49g.matrix
+RepeatMasker/Matrices/crossmatch/25p51g.matrix
+RepeatMasker/Matrices/crossmatch/25p53g.matrix
+RepeatMasker/Matrices/crossmatch/30p53g.matrix
+RepeatMasker/Matrices/crossmatch/at.matrix
+RepeatMasker/Matrices/crossmatch/identity.matrix
+RepeatMasker/Matrices/crossmatch/simple.matrix
+RepeatMasker/Matrices/crossmatch/simple1.matrix
+RepeatMasker/Matrices/crossmatch/transp.matrix
+RepeatMasker/Matrices/ncbi/nt/14p35g.matrix
+RepeatMasker/Matrices/ncbi/nt/14p37g.matrix
+RepeatMasker/Matrices/ncbi/nt/14p39g.matrix
+RepeatMasker/Matrices/ncbi/nt/14p41g.matrix
+RepeatMasker/Matrices/ncbi/nt/14p43g.matrix
+RepeatMasker/Matrices/ncbi/nt/14p45g.matrix
+RepeatMasker/Matrices/ncbi/nt/14p47g.matrix
+RepeatMasker/Matrices/ncbi/nt/14p49g.matrix
+RepeatMasker/Matrices/ncbi/nt/14p51g.matrix
+RepeatMasker/Matrices/ncbi/nt/14p53g.matrix
+RepeatMasker/Matrices/ncbi/nt/18p35g.matrix
+RepeatMasker/Matrices/ncbi/nt/18p37g.matrix
+RepeatMasker/Matrices/ncbi/nt/18p39g.matrix
+RepeatMasker/Matrices/ncbi/nt/18p41g.matrix
+RepeatMasker/Matrices/ncbi/nt/18p43g.matrix
+RepeatMasker/Matrices/ncbi/nt/18p45g.matrix
+RepeatMasker/Matrices/ncbi/nt/18p47g.matrix
+RepeatMasker/Matrices/ncbi/nt/18p49g.matrix
+RepeatMasker/Matrices/ncbi/nt/18p51g.matrix
+RepeatMasker/Matrices/ncbi/nt/18p53g.matrix
+RepeatMasker/Matrices/ncbi/nt/20p35g.matrix
+RepeatMasker/Matrices/ncbi/nt/20p37g.matrix
+RepeatMasker/Matrices/ncbi/nt/20p39g.matrix
+RepeatMasker/Matrices/ncbi/nt/20p41g.matrix
+RepeatMasker/Matrices/ncbi/nt/20p43g.matrix
+RepeatMasker/Matrices/ncbi/nt/20p45g.matrix
+RepeatMasker/Matrices/ncbi/nt/20p47g.matrix
+RepeatMasker/Matrices/ncbi/nt/20p49g.matrix
+RepeatMasker/Matrices/ncbi/nt/20p51g.matrix
+RepeatMasker/Matrices/ncbi/nt/20p53g.matrix
+RepeatMasker/Matrices/ncbi/nt/25p35g.matrix
+RepeatMasker/Matrices/ncbi/nt/25p37g.matrix
+RepeatMasker/Matrices/ncbi/nt/25p39g.matrix
+RepeatMasker/Matrices/ncbi/nt/25p41g.matrix
+RepeatMasker/Matrices/ncbi/nt/25p43g.matrix
+RepeatMasker/Matrices/ncbi/nt/25p45g.matrix
+RepeatMasker/Matrices/ncbi/nt/25p47g.matrix
+RepeatMasker/Matrices/ncbi/nt/25p49g.matrix
+RepeatMasker/Matrices/ncbi/nt/25p51g.matrix
+RepeatMasker/Matrices/ncbi/nt/25p53g.matrix
+RepeatMasker/Matrices/ncbi/nt/30p53g.matrix
+RepeatMasker/Matrices/ncbi/nt/at.matrix
+RepeatMasker/Matrices/ncbi/nt/atx.matrix
+RepeatMasker/Matrices/ncbi/nt/identity.matrix
+RepeatMasker/Matrices/ncbi/nt/ncbiblastdefault.matrix
+RepeatMasker/Matrices/ncbi/nt/simple.matrix
+RepeatMasker/Matrices/ncbi/nt/simple1.matrix
+RepeatMasker/Matrices/ncbi/nt/simplex.matrix
+RepeatMasker/Matrices/ncbi/nt/wublastdefault.matrix
+RepeatMasker/Matrices/wublast/aa/14p35g.matrix
+RepeatMasker/Matrices/wublast/aa/14p37g.matrix
+RepeatMasker/Matrices/wublast/aa/14p39g.matrix
+RepeatMasker/Matrices/wublast/aa/14p41g.matrix
+RepeatMasker/Matrices/wublast/aa/14p43g.matrix
+RepeatMasker/Matrices/wublast/aa/14p45g.matrix
+RepeatMasker/Matrices/wublast/aa/14p47g.matrix
+RepeatMasker/Matrices/wublast/aa/14p49g.matrix
+RepeatMasker/Matrices/wublast/aa/14p51g.matrix
+RepeatMasker/Matrices/wublast/aa/14p53g.matrix
+RepeatMasker/Matrices/wublast/aa/18p35g.matrix
+RepeatMasker/Matrices/wublast/aa/18p37g.matrix
+RepeatMasker/Matrices/wublast/aa/18p39g.matrix
+RepeatMasker/Matrices/wublast/aa/18p41g.matrix
+RepeatMasker/Matrices/wublast/aa/18p43g.matrix
+RepeatMasker/Matrices/wublast/aa/18p45g.matrix
+RepeatMasker/Matrices/wublast/aa/18p47g.matrix
+RepeatMasker/Matrices/wublast/aa/18p49g.matrix
+RepeatMasker/Matrices/wublast/aa/18p51g.matrix
+RepeatMasker/Matrices/wublast/aa/18p53g.matrix
+RepeatMasker/Matrices/wublast/aa/20p35g.matrix
+RepeatMasker/Matrices/wublast/aa/20p37g.matrix
+RepeatMasker/Matrices/wublast/aa/20p39g.matrix
+RepeatMasker/Matrices/wublast/aa/20p41g.matrix
+RepeatMasker/Matrices/wublast/aa/20p43g.matrix
+RepeatMasker/Matrices/wublast/aa/20p45g.matrix
+RepeatMasker/Matrices/wublast/aa/20p47g.matrix
+RepeatMasker/Matrices/wublast/aa/20p49g.matrix
+RepeatMasker/Matrices/wublast/aa/20p51g.matrix
+RepeatMasker/Matrices/wublast/aa/20p53g.matrix
+RepeatMasker/Matrices/wublast/aa/25p35g.matrix
+RepeatMasker/Matrices/wublast/aa/25p37g.matrix
+RepeatMasker/Matrices/wublast/aa/25p39g.matrix
+RepeatMasker/Matrices/wublast/aa/25p41g.matrix
+RepeatMasker/Matrices/wublast/aa/25p43g.matrix
+RepeatMasker/Matrices/wublast/aa/25p45g.matrix
+RepeatMasker/Matrices/wublast/aa/25p47g.matrix
+RepeatMasker/Matrices/wublast/aa/25p49g.matrix
+RepeatMasker/Matrices/wublast/aa/25p51g.matrix
+RepeatMasker/Matrices/wublast/aa/25p53g.matrix
+RepeatMasker/Matrices/wublast/aa/30p53g.matrix
+RepeatMasker/Matrices/wublast/aa/at.matrix
+RepeatMasker/Matrices/wublast/aa/identity.matrix
+RepeatMasker/Matrices/wublast/aa/simple.matrix
+RepeatMasker/Matrices/wublast/aa/simple1.matrix
+RepeatMasker/Matrices/wublast/nt/14p35g.matrix
+RepeatMasker/Matrices/wublast/nt/14p35g.matrix.4.2
+RepeatMasker/Matrices/wublast/nt/14p35g.matrix.4.4
+RepeatMasker/Matrices/wublast/nt/20p41g.matrix
+RepeatMasker/Matrices/wublast/nt/20p41g.matrix.4.2
+RepeatMasker/Matrices/wublast/nt/20p41g.matrix.4.4
+RepeatMasker/Matrix.pm
+RepeatMasker/NCBIBlastSearchEngine.pm
+RepeatMasker/NCBIBlastXSearchEngine.pm
+RepeatMasker/PRSearchResult.pm
+RepeatMasker/ProcessRepeats
+RepeatMasker/PubRef.pm
+RepeatMasker/RepbaseEMBL.pm
+RepeatMasker/RepbaseRecord.pm
+RepeatMasker/RepeatMasker
+RepeatMasker/RepeatMaskerConfig.pm
+RepeatMasker/RepeatMaskerConfig.pm.bak
+RepeatMasker/RepeatProteinMask
+RepeatMasker/RepeatRecord.pm
+RepeatMasker/SearchEngineI.pm
+RepeatMasker/SearchResult.pm
+RepeatMasker/SearchResultCollection.pm
+RepeatMasker/SeqDBI.pm
+RepeatMasker/SimpleBatcher.pm
+RepeatMasker/TRF.pm
+RepeatMasker/TRFResult.pm
+RepeatMasker/TRFSearchResult.pm
+RepeatMasker/Taxonomy.pm
+RepeatMasker/WUBlastSearchEngine.pm
+RepeatMasker/WUBlastXSearchEngine.pm
+RepeatMasker/addRepBase.pl
+RepeatMasker/bluegrad.jpg
+RepeatMasker/configure
+RepeatMasker/famdb.py
+RepeatMasker/util/RM2Bed.py
+RepeatMasker/util/buildRMLibFromEMBL.pl
+RepeatMasker/util/buildSummary.pl
+RepeatMasker/util/calcDivergenceFromAlign.pl
+RepeatMasker/util/createRepeatLandscape.pl
+RepeatMasker/util/dupliconToSVG.pl
+RepeatMasker/util/getRepeatMaskerBatch.pl
+RepeatMasker/util/maskFile.pl
+RepeatMasker/util/rmOut2Fasta.pl
+RepeatMasker/util/rmOutToGFF3.pl
+RepeatMasker/util/rmToUCSCTables.pl
+RepeatMasker/util/trfMask
+RepeatMasker/util/wublastToCrossmatch.pl
+share/doc/RepeatMasker/README.md
+share/doc/RepeatMasker/daterepeats.help
+share/doc/RepeatMasker/repeatmasker.help
diff --git a/repeatmasker/distinfo b/repeatmasker/distinfo
new file mode 100644
index 0000000000..53e1e9dc7e
--- /dev/null
+++ b/repeatmasker/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (RepeatMasker-4.1.2-p1.tar.gz) = 0fb73acde3206b18fb687aa30caea9578230b1f9
+RMD160 (RepeatMasker-4.1.2-p1.tar.gz) = bba59a9ca8b2c069618d1058e1d440a37d93f544
+SHA512 (RepeatMasker-4.1.2-p1.tar.gz) = 3cab3c8a3b04daef5fd2a8fcb906609591360551632d865443e56929130352ac7d422fbcb4d75b8e2768ff8bf1fb133392f4333f0b54abd3704080b9e8223415
+Size (RepeatMasker-4.1.2-p1.tar.gz) = 350397633 bytes
+SHA1 (patch-configure) = d3d7024457c2e93efd3b29237625d39e05142ffc
diff --git a/repeatmasker/patches/patch-configure b/repeatmasker/patches/patch-configure
new file mode 100644
index 0000000000..a7b40f4efb
--- /dev/null
+++ b/repeatmasker/patches/patch-configure
@@ -0,0 +1,24 @@
+$NetBSD$
+
+Replace "python3" with @PYTHONBIN@ (later substituted for the actual
+path) so configure finds it.
+
+--- configure.orig	2021-04-01 15:45:09.000000000 +0000
++++ configure
+@@ -236,12 +236,12 @@
+ }
+ 
+ #
+-# Test python3 and h5py
++# Test @PYTHONBIN@ and h5py
+ #
+-system('python3 -c "import h5py"');
++system('@PYTHONBIN@ -c "import h5py"');
+ if ( $? ) {
+-  print "\nPython3 and the h5py module is a pre-requisite for RepeatMasker.\n" 
+-      . "Either python3 could not be found in your path or h5py is not installed.\n"
++  print "\n@PYTHONBIN@ and the h5py module is a pre-requisite for RepeatMasker.\n" 
++      . "Either @PYTHONBIN@ could not be found in your path or h5py is not installed.\n"
+       . "Please very both before rerunning configure.\n\n";
+ }
+
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