'Add microbiomeutil: Utilities for processing and analyzing 16S rRNA genes'

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: 'Add microbiomeutil: Utilities for processing and analyzing 16S rRNA genes'
From: Jason Bacon <bacon@centosdev.local>
Date: Thu, 30 Mar 2017 17:06:59 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon@centosdev.local>
Pushed By:	outpaddling
Date:		Thu Mar 30 12:06:59 2017 -0500
Changeset:	e3c975a72a191863efc657c8cd0845151d2a5a3a

Modified Files:
	Makefile
Added Files:
	microbiomeutil/DESCR
	microbiomeutil/Makefile
	microbiomeutil/PLIST
	microbiomeutil/TODO
	microbiomeutil/buildlink3.mk
	microbiomeutil/distinfo
	microbiomeutil/files/modulefile
	microbiomeutil/patches/patch-NAST-iEr_NAST-iEr.c

Log Message:
'Add microbiomeutil: 	Utilities for processing and analyzing 16S rRNA genes'

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e3c975a72a191863efc657c8cd0845151d2a5a3a

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

diffstat:
 Makefile                                         |   1 +
 microbiomeutil/DESCR                             |   5 +
 microbiomeutil/Makefile                          |  57 +++++++++
 microbiomeutil/PLIST                             | 147 +++++++++++++++++++++++
 microbiomeutil/TODO                              |   1 +
 microbiomeutil/buildlink3.mk                     |  12 ++
 microbiomeutil/distinfo                          |   6 +
 microbiomeutil/files/modulefile                  |  20 +++
 microbiomeutil/patches/patch-NAST-iEr_NAST-iEr.c |  10 ++
 9 files changed, 259 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 8853104900..199d461871 100644
--- a/Makefile
+++ b/Makefile
@@ -1863,6 +1863,7 @@ SUBDIR+=	metasploit
 SUBDIR+=	mg-cvs
 SUBDIR+=	mg-lsh
 SUBDIR+=	mic-paren
+SUBDIR+=	microbiomeutil
 SUBDIR+=	microblog-purple
 SUBDIR+=	microcom
 SUBDIR+=	microtetris
diff --git a/microbiomeutil/DESCR b/microbiomeutil/DESCR
new file mode 100644
index 0000000000..b529f3410f
--- /dev/null
+++ b/microbiomeutil/DESCR
@@ -0,0 +1,5 @@
+A set of software utilities for processing and analyzing 16S rRNA genes
+including generating NAST alignments, chimera checking, and assembling paired
+16S rRNA reads according to reference sequence homology.
+
+WWW: http://sourceforge.net/projects/microbiomeutil/
diff --git a/microbiomeutil/Makefile b/microbiomeutil/Makefile
new file mode 100644
index 0000000000..f2a3c6e4c2
--- /dev/null
+++ b/microbiomeutil/Makefile
@@ -0,0 +1,57 @@
+# $NetBSD$
+
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+DISTNAME=	microbiomeutil-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=microbiomeutil/}
+EXTRACT_SUFX=	.tgz
+
+MAINTAINER=	dsiercks%uwm.edu@localhost
+
+COMMENT=	Utilities for processing and analyzing 16S rRNA genes
+#LICENSE=	BSD4CLAUSE
+
+# Pessimistic assumption.  Test and change if possible.
+MAKE_JOBS_SAFE=	no
+
+#ONLY_FOR_PLATFORM=	
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	pax
+
+# Adapt REINPLACE commands to SUBST:
+SUBST_CLASSES+=		gcc
+SUBST_STAGE.gcc=	post-patch
+SUBST_FILES.gcc=	${WRKSRC}/NAST-iEr/Makefile
+SUBST_SED.gcc=		-e 's|gcc|$${CC}|g'
+
+PORTVERSION=	r20110519
+
+# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
+#.include "../../mk/bsd.prefs.mk"
+
+# Keep this if there are user-selectable options.
+#.include "options.mk"
+
+# You may need this, especially if using do-install.
+
+# Note: Depends on PLIST.
+#AUTO_MKDIRS=	yes
+
+MODULE_PATH=	etc/modulefiles/${PORTNAME}/${PORTVERSION}
+PORTNAME=	microbiomutil
+
+do-install:
+	${MKDIR} ${DESTDIR}${PREFIX}/${PORTNAME}
+	${MKDIR} ${DESTDIR}${PREFIX}/etc/modulefiles/${PORTNAME}
+	${INSTALL_SCRIPT} ${FILESDIR}/modulefile \
+		${DESTDIR}${PREFIX}/${MODULE_PATH}
+	cd ${WRKSRC} && pax -rw \
+		AmosCmp16Spipeline ChimeraSlayer NAST-iEr TreeChopper WigeoN RESOURCES ${DESTDIR}${PREFIX}/${PORTNAME}
+
+.include "../../wip/cdbfasta/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/microbiomeutil/PLIST b/microbiomeutil/PLIST
new file mode 100644
index 0000000000..b5a35b8e06
--- /dev/null
+++ b/microbiomeutil/PLIST
@@ -0,0 +1,147 @@
+@comment $NetBSD$
+etc/modulefiles/microbiomutil/${PKGVERSION}
+microbiomutil/AmosCmp16Spipeline/AmosPatch/AMOScmp
+microbiomutil/AmosCmp16Spipeline/LICENSE
+microbiomutil/AmosCmp16Spipeline/PyLib/CdbTools.py
+microbiomutil/AmosCmp16Spipeline/PyLib/CmdRunner.py
+microbiomutil/AmosCmp16Spipeline/PyLib/FastaReader.py
+microbiomutil/AmosCmp16Spipeline/PyLib/contig_layout_to_scaffold.py
+microbiomutil/AmosCmp16Spipeline/PyLib/contig_layout_to_scaffold.pyc
+microbiomutil/AmosCmp16Spipeline/PyLib/homology_trim_lucy_output.py
+microbiomutil/AmosCmp16Spipeline/PyLib/homology_trim_lucy_output.pyc
+microbiomutil/AmosCmp16Spipeline/README
+microbiomutil/AmosCmp16Spipeline/__conf.txt
+microbiomutil/AmosCmp16Spipeline/amosCmp16Spipeline.py
+microbiomutil/AmosCmp16Spipeline/conf.txt
+microbiomutil/AmosCmp16Spipeline/sample_data/HMP_MOCK_16S_references.fasta
+microbiomutil/AmosCmp16Spipeline/sample_data/HMP_MOCK_16S_references.fasta.cidx
+microbiomutil/AmosCmp16Spipeline/sample_data/HMP_MOCK_16S_references.fasta.nhr
+microbiomutil/AmosCmp16Spipeline/sample_data/HMP_MOCK_16S_references.fasta.nin
+microbiomutil/AmosCmp16Spipeline/sample_data/HMP_MOCK_16S_references.fasta.nsq
+microbiomutil/AmosCmp16Spipeline/sample_data/reads.fasta
+microbiomutil/AmosCmp16Spipeline/sample_data/reads.fasta.asm.log
+microbiomutil/AmosCmp16Spipeline/sample_data/reads.fasta.asm.quals
+microbiomutil/AmosCmp16Spipeline/sample_data/reads.fasta.asm.seqs
+microbiomutil/AmosCmp16Spipeline/sample_data/reads.fasta.cidx
+microbiomutil/AmosCmp16Spipeline/sample_data/reads.pairs
+microbiomutil/AmosCmp16Spipeline/sample_data/reads.quals
+microbiomutil/AmosCmp16Spipeline/sample_data/reads.quals.cidx
+microbiomutil/AmosCmp16Spipeline/sample_data/runMe.sh
+microbiomutil/ChimeraSlayer/ChimeraParentSelector/CM_plotter.pl
+microbiomutil/ChimeraSlayer/ChimeraParentSelector/CPC_to_CPS.pl
+microbiomutil/ChimeraSlayer/ChimeraParentSelector/CPS_to_RENAST.pl
+microbiomutil/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl
+microbiomutil/ChimeraSlayer/ChimeraParentSelector/run_chimeraParentSelector.pl
+microbiomutil/ChimeraSlayer/ChimeraPhyloChecker/CPS_to_CPC.pl
+microbiomutil/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl
+microbiomutil/ChimeraSlayer/ChimeraSlayer.pl
+microbiomutil/ChimeraSlayer/LICENSE
+microbiomutil/ChimeraSlayer/Makefile
+microbiomutil/ChimeraSlayer/PerlLib/AlignCompare.pm
+microbiomutil/ChimeraSlayer/PerlLib/BHStats.pm
+microbiomutil/ChimeraSlayer/PerlLib/CdbTools.pm
+microbiomutil/ChimeraSlayer/PerlLib/Fasta_reader.pm
+microbiomutil/ChimeraSlayer/PerlLib/NAST_to_Eco_coords.pm
+microbiomutil/ChimeraSlayer/PerlLib/TaxonomyGraph.pm
+microbiomutil/ChimeraSlayer/__BroadBellerophon/BellerophonGG.pl
+microbiomutil/ChimeraSlayer/__BroadBellerophon/masks/eco.prokMSA
+microbiomutil/ChimeraSlayer/__BroadBellerophon/masks/lanemask.NAST
+microbiomutil/ChimeraSlayer/__BroadBellerophon/run_bellerophon_prog.pl
+microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/NAST_evolve.pl
+microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/PerID_Pairs_All_vs_All.pl
+microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/PerID_Pairs_via_Taxonomy.pl
+microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/ROC_writer.pl
+microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/SeqSubstrates/rRNA16S.toChimerize.PerID_compare
+microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/SeqSubstrates/rRNA16S.toChimerize.fasta
+microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/SeqSubstrates/rRNA16S.toChimerize.fasta.NAST
+microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/SeqSubstrates/rRNA16S.toChimerize.taxonomy
+microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/art_chimera_constructor.pl
+microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/chimera_control_extractor.pl
+microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/simple_art_chimera_constructor.pl
+microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/write_100_chimeras_per_div.pl
+microbiomutil/ChimeraSlayer/__KmerChimerDetector/KmerChimerDetector.pl
+microbiomutil/ChimeraSlayer/sample_data/Makefile
+microbiomutil/ChimeraSlayer/sample_data/chims.NAST
+microbiomutil/ChimeraSlayer/sample_data/runMe.sh
+microbiomutil/ChimeraSlayer/util/CMCS_to_treeImg.pl
+microbiomutil/ChimeraSlayer/util/CS_add_taxonomy.pl
+microbiomutil/ChimeraSlayer/util/breakpoint_to_profile.pl
+microbiomutil/ChimeraSlayer/util/merge_CM_CS_outputs.pl
+microbiomutil/ChimeraSlayer/util/merge_CS_n_CM_breakpoints.pl
+microbiomutil/NAST-iEr/LICENSE
+microbiomutil/NAST-iEr/Makefile
+microbiomutil/NAST-iEr/NAST-iEr
+microbiomutil/NAST-iEr/NAST-iEr.c
+microbiomutil/NAST-iEr/PerlLib/CdbTools.pm
+microbiomutil/NAST-iEr/PerlLib/Fasta_reader.pm
+microbiomutil/NAST-iEr/PerlLib/Nuc_translator.pm
+microbiomutil/NAST-iEr/README
+microbiomutil/NAST-iEr/iterative_refinement/compare_DBs.pl
+microbiomutil/NAST-iEr/iterative_refinement/iteratively_realign_db_selfsearch.pl
+microbiomutil/NAST-iEr/iterative_refinement/quant_differences.pl
+microbiomutil/NAST-iEr/run_NAST-iEr.pl
+microbiomutil/NAST-iEr/sample_data/Makefile
+microbiomutil/NAST-iEr/sample_data/formatdb.log
+microbiomutil/NAST-iEr/sample_data/query_seq.fasta
+microbiomutil/NAST-iEr/sample_data/runMe.sh
+microbiomutil/NAST-iEr/sample_data/template_seqs.NAST
+microbiomutil/NAST-iEr/sample_data/testForUtils.pl
+microbiomutil/NAST-iEr/util/apply_NAST_MASK.pl
+microbiomutil/NAST-iEr/util/masks/eco.prokMSA
+microbiomutil/NAST-iEr/util/masks/lanemask.NAST
+microbiomutil/NAST-iEr/util/mfasta_remove_allGapCols.pl
+microbiomutil/NAST-iEr/util/mfasta_remove_gaps.pl
+microbiomutil/NAST-iEr/util/show_malign_no_gap.pl
+microbiomutil/NAST-iEr/util/show_malign_no_gap_no_identical_cols.pl
+microbiomutil/RESOURCES/Makefile
+microbiomutil/RESOURCES/RDP/classifier_data_dir/bergeyTrainingTree.xml
+microbiomutil/RESOURCES/RDP/classifier_data_dir/genus_wordConditionalProbList.txt
+microbiomutil/RESOURCES/RDP/classifier_data_dir/logWordPrior.txt
+microbiomutil/RESOURCES/RDP/classifier_data_dir/rRNAClassifier.properties
+microbiomutil/RESOURCES/RDP/classifier_data_dir/wordConditionalProbIndexArr.txt
+microbiomutil/RESOURCES/RDP/util/RDP_tack_classification_onto_fasta_header.pl
+microbiomutil/RESOURCES/RDP/util/RDP_to_tab.pl
+microbiomutil/RESOURCES/README
+microbiomutil/RESOURCES/accs
+microbiomutil/RESOURCES/formatdb.log
+microbiomutil/RESOURCES/identify_conflicting_taxons.pl
+microbiomutil/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta
+microbiomutil/RESOURCES/rRNA16S.gold.fasta
+microbiomutil/RESOURCES/rRNA16S.gold.taxonomy
+microbiomutil/RESOURCES/results
+microbiomutil/TreeChopper/LICENSE
+microbiomutil/TreeChopper/README.txt
+microbiomutil/TreeChopper/sample_data/2percent.OTUs
+microbiomutil/TreeChopper/sample_data/2percent.j0.7.OTUs
+microbiomutil/TreeChopper/sample_data/mockref.RDPNAST.tree
+microbiomutil/TreeChopper/sample_data/output_0.02_0.7.OTUs
+microbiomutil/TreeChopper/sample_data/runMe.sh
+microbiomutil/TreeChopper/treeChopper.pl
+microbiomutil/TreeChopper/util/print.pl
+microbiomutil/TreeChopper/util/slclust
+microbiomutil/TreeChopper/util/tree_leaf_pairs_within_dist.pl
+microbiomutil/TreeChopper/util/tree_report_nodes.pl
+microbiomutil/WigeoN/LICENSE
+microbiomutil/WigeoN/Makefile
+microbiomutil/WigeoN/PerlLib/BHStats.pm
+microbiomutil/WigeoN/PerlLib/CdbTools.pm
+microbiomutil/WigeoN/PerlLib/Fasta_reader.pm
+microbiomutil/WigeoN/README
+microbiomutil/WigeoN/WigeoN.pl
+microbiomutil/WigeoN/data/DE_quantiles.dat
+microbiomutil/WigeoN/data/WigeoN.AllVsAllReferences.txt.gz
+microbiomutil/WigeoN/data/eco.prokMSA
+microbiomutil/WigeoN/data/rRNA16S.gold.NAST_ALIGNED.fasta.cons
+microbiomutil/WigeoN/run_CM_to_WigeoN.pl
+microbiomutil/WigeoN/run_WigeoN.pl
+microbiomutil/WigeoN/sample_data/Makefile
+microbiomutil/WigeoN/sample_data/chims.NAST
+microbiomutil/WigeoN/sample_data/runMe.sh
+microbiomutil/WigeoN/util/all_vs_all_WigeoN.mod.pl
+microbiomutil/WigeoN/util/all_vs_all_WigeoN.pl
+microbiomutil/WigeoN/util/apply_eco_Mask.pl
+microbiomutil/WigeoN/util/compute_quant_bins.pl
+microbiomutil/WigeoN/util/eco.prokMSA
+microbiomutil/WigeoN/util/eco_nast_freq.pl
+microbiomutil/WigeoN/util/makeConservationProfile.pl
+microbiomutil/WigeoN/util/smooth.pl
diff --git a/microbiomeutil/TODO b/microbiomeutil/TODO
new file mode 100644
index 0000000000..b687356e6b
--- /dev/null
+++ b/microbiomeutil/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/microbiomeutil/buildlink3.mk b/microbiomeutil/buildlink3.mk
new file mode 100644
index 0000000000..2d30e4810f
--- /dev/null
+++ b/microbiomeutil/buildlink3.mk
@@ -0,0 +1,12 @@
+# $NetBSD$
+
+BUILDLINK_TREE+=	microbiomeutil
+
+.if !defined(MICROBIOMEUTIL_BUILDLINK3_MK)
+MICROBIOMEUTIL_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.microbiomeutil+=	microbiomeutil>=r20110519
+BUILDLINK_PKGSRCDIR.microbiomeutil?=	../../wip/microbiomeutil
+.endif	# MICROBIOMEUTIL_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-microbiomeutil
diff --git a/microbiomeutil/distinfo b/microbiomeutil/distinfo
new file mode 100644
index 0000000000..9e4126c793
--- /dev/null
+++ b/microbiomeutil/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (microbiomeutil-r20110519.tgz) = 57fb144de76152447abbe3929357ff8bb887b130
+RMD160 (microbiomeutil-r20110519.tgz) = b3ff65fccf53cbfb3020c2071832c2deea9aa800
+SHA512 (microbiomeutil-r20110519.tgz) = 10965fe45739d8c8395c6e15b67a7057c299336bf7498a99ee12cd6ae96d393b9f92a55485b9a8b621ee276bbe61c11299d94fe3c0de88e1b92aeb546a85fc9f
+Size (microbiomeutil-r20110519.tgz) = 133623556 bytes
diff --git a/microbiomeutil/files/modulefile b/microbiomeutil/files/modulefile
new file mode 100644
index 0000000000..d8d2608328
--- /dev/null
+++ b/microbiomeutil/files/modulefile
@@ -0,0 +1,20 @@
+#%Module1.0#####################################################################
+##
+## modules modulefile
+##
+## modulefiles/modules.  Generated from modules.in by configure.
+##
+proc ModulesHelp { } {
+        puts stderr "\tApplication: microbiomeutil r20110519"
+}
+
+module-whatis	"microbiomeutil"
+
+set	version		2011.05.19
+set	appsroot	/usr/local/microbiomeutil
+
+prepend-path    PATH   		$appsroot/ChimeraSlayer
+prepend-path	PATH		$appsroot/NAST-iEr
+prepend-path	PATH		$appsroot/TreeChopper
+prepend-path	PATH		$appsroot/WigeoN	
+prepend-path	PATH		$appsroot/AmosCmp16Spipeline
diff --git a/microbiomeutil/patches/patch-NAST-iEr_NAST-iEr.c b/microbiomeutil/patches/patch-NAST-iEr_NAST-iEr.c
new file mode 100644
index 0000000000..8180a83656
--- /dev/null
+++ b/microbiomeutil/patches/patch-NAST-iEr_NAST-iEr.c
@@ -0,0 +1,10 @@
+$NetBSD$
+
+--- NAST-iEr/NAST-iEr.c.orig	2015-02-24 16:16:28.667021760 -0600
++++ NAST-iEr/NAST-iEr.c	2015-02-24 16:16:40.213027838 -0600
+@@ -1,4 +1,5 @@
+ #include <stdlib.h>
++#include <ctype.h>
+ #include <stdio.h>
+ #include <string.h>
+ #include <unistd.h>
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