'Add microbiomeutil: Utilities for processing and analyzing 16S rRNA genes'
This commit is contained in:
Jason Bacon
parent
378948b5cf
commit
e3c975a72a
1
Makefile
1
Makefile
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@ -1863,6 +1863,7 @@ SUBDIR+= metasploit
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SUBDIR+= mg-cvs
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SUBDIR+= mg-lsh
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SUBDIR+= mic-paren
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SUBDIR+= microbiomeutil
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SUBDIR+= microblog-purple
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SUBDIR+= microcom
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SUBDIR+= microtetris
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5
microbiomeutil/DESCR
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5
microbiomeutil/DESCR
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@ -0,0 +1,5 @@
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A set of software utilities for processing and analyzing 16S rRNA genes
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including generating NAST alignments, chimera checking, and assembling paired
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16S rRNA reads according to reference sequence homology.
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WWW: http://sourceforge.net/projects/microbiomeutil/
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57
microbiomeutil/Makefile
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57
microbiomeutil/Makefile
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@ -0,0 +1,57 @@
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# $NetBSD$
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###########################################################
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# Generated by fbsd2pkg #
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###########################################################
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DISTNAME= microbiomeutil-${PORTVERSION}
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CATEGORIES= biology
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MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=microbiomeutil/}
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EXTRACT_SUFX= .tgz
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MAINTAINER= dsiercks@uwm.edu
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COMMENT= Utilities for processing and analyzing 16S rRNA genes
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#LICENSE= BSD4CLAUSE
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# Pessimistic assumption. Test and change if possible.
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MAKE_JOBS_SAFE= no
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#ONLY_FOR_PLATFORM=
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# Just assuming C and C++: Adjust this!
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USE_LANGUAGES= c c++
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USE_TOOLS+= pax
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# Adapt REINPLACE commands to SUBST:
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SUBST_CLASSES+= gcc
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SUBST_STAGE.gcc= post-patch
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SUBST_FILES.gcc= ${WRKSRC}/NAST-iEr/Makefile
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SUBST_SED.gcc= -e 's|gcc|$${CC}|g'
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PORTVERSION= r20110519
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# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
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#.include "../../mk/bsd.prefs.mk"
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# Keep this if there are user-selectable options.
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#.include "options.mk"
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# You may need this, especially if using do-install.
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# Note: Depends on PLIST.
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#AUTO_MKDIRS= yes
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MODULE_PATH= etc/modulefiles/${PORTNAME}/${PORTVERSION}
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PORTNAME= microbiomutil
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do-install:
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${MKDIR} ${DESTDIR}${PREFIX}/${PORTNAME}
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${MKDIR} ${DESTDIR}${PREFIX}/etc/modulefiles/${PORTNAME}
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${INSTALL_SCRIPT} ${FILESDIR}/modulefile \
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${DESTDIR}${PREFIX}/${MODULE_PATH}
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cd ${WRKSRC} && pax -rw \
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AmosCmp16Spipeline ChimeraSlayer NAST-iEr TreeChopper WigeoN RESOURCES ${DESTDIR}${PREFIX}/${PORTNAME}
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.include "../../wip/cdbfasta/buildlink3.mk"
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.include "../../mk/bsd.pkg.mk"
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147
microbiomeutil/PLIST
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147
microbiomeutil/PLIST
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@ -0,0 +1,147 @@
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@comment $NetBSD$
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etc/modulefiles/microbiomutil/${PKGVERSION}
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microbiomutil/AmosCmp16Spipeline/AmosPatch/AMOScmp
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microbiomutil/AmosCmp16Spipeline/LICENSE
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microbiomutil/AmosCmp16Spipeline/PyLib/CdbTools.py
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microbiomutil/AmosCmp16Spipeline/PyLib/CmdRunner.py
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microbiomutil/AmosCmp16Spipeline/PyLib/FastaReader.py
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microbiomutil/AmosCmp16Spipeline/PyLib/contig_layout_to_scaffold.py
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microbiomutil/AmosCmp16Spipeline/PyLib/contig_layout_to_scaffold.pyc
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microbiomutil/AmosCmp16Spipeline/PyLib/homology_trim_lucy_output.py
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microbiomutil/AmosCmp16Spipeline/PyLib/homology_trim_lucy_output.pyc
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microbiomutil/AmosCmp16Spipeline/README
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microbiomutil/AmosCmp16Spipeline/__conf.txt
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microbiomutil/AmosCmp16Spipeline/amosCmp16Spipeline.py
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microbiomutil/AmosCmp16Spipeline/conf.txt
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microbiomutil/AmosCmp16Spipeline/sample_data/HMP_MOCK_16S_references.fasta
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microbiomutil/AmosCmp16Spipeline/sample_data/HMP_MOCK_16S_references.fasta.cidx
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microbiomutil/AmosCmp16Spipeline/sample_data/HMP_MOCK_16S_references.fasta.nhr
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microbiomutil/AmosCmp16Spipeline/sample_data/HMP_MOCK_16S_references.fasta.nin
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microbiomutil/AmosCmp16Spipeline/sample_data/HMP_MOCK_16S_references.fasta.nsq
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microbiomutil/AmosCmp16Spipeline/sample_data/reads.fasta
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microbiomutil/AmosCmp16Spipeline/sample_data/reads.fasta.asm.log
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microbiomutil/AmosCmp16Spipeline/sample_data/reads.fasta.asm.quals
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microbiomutil/AmosCmp16Spipeline/sample_data/reads.fasta.asm.seqs
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microbiomutil/AmosCmp16Spipeline/sample_data/reads.fasta.cidx
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microbiomutil/AmosCmp16Spipeline/sample_data/reads.pairs
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microbiomutil/AmosCmp16Spipeline/sample_data/reads.quals
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microbiomutil/AmosCmp16Spipeline/sample_data/reads.quals.cidx
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microbiomutil/AmosCmp16Spipeline/sample_data/runMe.sh
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microbiomutil/ChimeraSlayer/ChimeraParentSelector/CM_plotter.pl
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microbiomutil/ChimeraSlayer/ChimeraParentSelector/CPC_to_CPS.pl
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microbiomutil/ChimeraSlayer/ChimeraParentSelector/CPS_to_RENAST.pl
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microbiomutil/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl
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microbiomutil/ChimeraSlayer/ChimeraParentSelector/run_chimeraParentSelector.pl
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microbiomutil/ChimeraSlayer/ChimeraPhyloChecker/CPS_to_CPC.pl
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microbiomutil/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl
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microbiomutil/ChimeraSlayer/ChimeraSlayer.pl
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microbiomutil/ChimeraSlayer/LICENSE
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microbiomutil/ChimeraSlayer/Makefile
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microbiomutil/ChimeraSlayer/PerlLib/AlignCompare.pm
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microbiomutil/ChimeraSlayer/PerlLib/BHStats.pm
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microbiomutil/ChimeraSlayer/PerlLib/CdbTools.pm
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microbiomutil/ChimeraSlayer/PerlLib/Fasta_reader.pm
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microbiomutil/ChimeraSlayer/PerlLib/NAST_to_Eco_coords.pm
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microbiomutil/ChimeraSlayer/PerlLib/TaxonomyGraph.pm
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microbiomutil/ChimeraSlayer/__BroadBellerophon/BellerophonGG.pl
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microbiomutil/ChimeraSlayer/__BroadBellerophon/masks/eco.prokMSA
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microbiomutil/ChimeraSlayer/__BroadBellerophon/masks/lanemask.NAST
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microbiomutil/ChimeraSlayer/__BroadBellerophon/run_bellerophon_prog.pl
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microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/NAST_evolve.pl
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microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/PerID_Pairs_All_vs_All.pl
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microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/PerID_Pairs_via_Taxonomy.pl
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microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/ROC_writer.pl
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microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/SeqSubstrates/rRNA16S.toChimerize.PerID_compare
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microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/SeqSubstrates/rRNA16S.toChimerize.fasta
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microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/SeqSubstrates/rRNA16S.toChimerize.fasta.NAST
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microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/SeqSubstrates/rRNA16S.toChimerize.taxonomy
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microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/art_chimera_constructor.pl
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microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/chimera_control_extractor.pl
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microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/simple_art_chimera_constructor.pl
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microbiomutil/ChimeraSlayer/__ChimeraConstructorToolkit/write_100_chimeras_per_div.pl
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microbiomutil/ChimeraSlayer/__KmerChimerDetector/KmerChimerDetector.pl
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microbiomutil/ChimeraSlayer/sample_data/Makefile
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microbiomutil/ChimeraSlayer/sample_data/chims.NAST
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microbiomutil/ChimeraSlayer/sample_data/runMe.sh
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microbiomutil/ChimeraSlayer/util/CMCS_to_treeImg.pl
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microbiomutil/ChimeraSlayer/util/CS_add_taxonomy.pl
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microbiomutil/ChimeraSlayer/util/breakpoint_to_profile.pl
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microbiomutil/ChimeraSlayer/util/merge_CM_CS_outputs.pl
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microbiomutil/ChimeraSlayer/util/merge_CS_n_CM_breakpoints.pl
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microbiomutil/NAST-iEr/LICENSE
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microbiomutil/NAST-iEr/Makefile
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microbiomutil/NAST-iEr/NAST-iEr
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microbiomutil/NAST-iEr/NAST-iEr.c
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microbiomutil/NAST-iEr/PerlLib/CdbTools.pm
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microbiomutil/NAST-iEr/PerlLib/Fasta_reader.pm
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microbiomutil/NAST-iEr/PerlLib/Nuc_translator.pm
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microbiomutil/NAST-iEr/README
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microbiomutil/NAST-iEr/iterative_refinement/compare_DBs.pl
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microbiomutil/NAST-iEr/iterative_refinement/iteratively_realign_db_selfsearch.pl
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microbiomutil/NAST-iEr/iterative_refinement/quant_differences.pl
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microbiomutil/NAST-iEr/run_NAST-iEr.pl
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microbiomutil/NAST-iEr/sample_data/Makefile
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microbiomutil/NAST-iEr/sample_data/formatdb.log
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microbiomutil/NAST-iEr/sample_data/query_seq.fasta
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microbiomutil/NAST-iEr/sample_data/runMe.sh
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microbiomutil/NAST-iEr/sample_data/template_seqs.NAST
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microbiomutil/NAST-iEr/sample_data/testForUtils.pl
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microbiomutil/NAST-iEr/util/apply_NAST_MASK.pl
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microbiomutil/NAST-iEr/util/masks/eco.prokMSA
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microbiomutil/NAST-iEr/util/masks/lanemask.NAST
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microbiomutil/NAST-iEr/util/mfasta_remove_allGapCols.pl
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microbiomutil/NAST-iEr/util/mfasta_remove_gaps.pl
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microbiomutil/NAST-iEr/util/show_malign_no_gap.pl
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microbiomutil/NAST-iEr/util/show_malign_no_gap_no_identical_cols.pl
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microbiomutil/RESOURCES/Makefile
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microbiomutil/RESOURCES/RDP/classifier_data_dir/bergeyTrainingTree.xml
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microbiomutil/RESOURCES/RDP/classifier_data_dir/genus_wordConditionalProbList.txt
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microbiomutil/RESOURCES/RDP/classifier_data_dir/logWordPrior.txt
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microbiomutil/RESOURCES/RDP/classifier_data_dir/rRNAClassifier.properties
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microbiomutil/RESOURCES/RDP/classifier_data_dir/wordConditionalProbIndexArr.txt
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microbiomutil/RESOURCES/RDP/util/RDP_tack_classification_onto_fasta_header.pl
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microbiomutil/RESOURCES/RDP/util/RDP_to_tab.pl
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microbiomutil/RESOURCES/README
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microbiomutil/RESOURCES/accs
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microbiomutil/RESOURCES/formatdb.log
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microbiomutil/RESOURCES/identify_conflicting_taxons.pl
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microbiomutil/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta
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microbiomutil/RESOURCES/rRNA16S.gold.fasta
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microbiomutil/RESOURCES/rRNA16S.gold.taxonomy
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microbiomutil/RESOURCES/results
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microbiomutil/TreeChopper/LICENSE
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microbiomutil/TreeChopper/README.txt
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microbiomutil/TreeChopper/sample_data/2percent.OTUs
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microbiomutil/TreeChopper/sample_data/2percent.j0.7.OTUs
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microbiomutil/TreeChopper/sample_data/mockref.RDPNAST.tree
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microbiomutil/TreeChopper/sample_data/output_0.02_0.7.OTUs
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microbiomutil/TreeChopper/sample_data/runMe.sh
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microbiomutil/TreeChopper/treeChopper.pl
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microbiomutil/TreeChopper/util/print.pl
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microbiomutil/TreeChopper/util/slclust
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microbiomutil/TreeChopper/util/tree_leaf_pairs_within_dist.pl
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microbiomutil/TreeChopper/util/tree_report_nodes.pl
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microbiomutil/WigeoN/LICENSE
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microbiomutil/WigeoN/Makefile
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microbiomutil/WigeoN/PerlLib/BHStats.pm
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microbiomutil/WigeoN/PerlLib/CdbTools.pm
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microbiomutil/WigeoN/PerlLib/Fasta_reader.pm
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microbiomutil/WigeoN/README
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microbiomutil/WigeoN/WigeoN.pl
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microbiomutil/WigeoN/data/DE_quantiles.dat
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microbiomutil/WigeoN/data/WigeoN.AllVsAllReferences.txt.gz
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microbiomutil/WigeoN/data/eco.prokMSA
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microbiomutil/WigeoN/data/rRNA16S.gold.NAST_ALIGNED.fasta.cons
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microbiomutil/WigeoN/run_CM_to_WigeoN.pl
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microbiomutil/WigeoN/run_WigeoN.pl
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microbiomutil/WigeoN/sample_data/Makefile
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microbiomutil/WigeoN/sample_data/chims.NAST
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microbiomutil/WigeoN/sample_data/runMe.sh
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microbiomutil/WigeoN/util/all_vs_all_WigeoN.mod.pl
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microbiomutil/WigeoN/util/all_vs_all_WigeoN.pl
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microbiomutil/WigeoN/util/apply_eco_Mask.pl
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microbiomutil/WigeoN/util/compute_quant_bins.pl
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microbiomutil/WigeoN/util/eco.prokMSA
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microbiomutil/WigeoN/util/eco_nast_freq.pl
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microbiomutil/WigeoN/util/makeConservationProfile.pl
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microbiomutil/WigeoN/util/smooth.pl
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1
microbiomeutil/TODO
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1
microbiomeutil/TODO
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Clean up and test
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12
microbiomeutil/buildlink3.mk
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12
microbiomeutil/buildlink3.mk
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@ -0,0 +1,12 @@
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# $NetBSD$
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BUILDLINK_TREE+= microbiomeutil
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.if !defined(MICROBIOMEUTIL_BUILDLINK3_MK)
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MICROBIOMEUTIL_BUILDLINK3_MK:=
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BUILDLINK_API_DEPENDS.microbiomeutil+= microbiomeutil>=r20110519
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BUILDLINK_PKGSRCDIR.microbiomeutil?= ../../wip/microbiomeutil
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.endif # MICROBIOMEUTIL_BUILDLINK3_MK
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BUILDLINK_TREE+= -microbiomeutil
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6
microbiomeutil/distinfo
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6
microbiomeutil/distinfo
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@ -0,0 +1,6 @@
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$NetBSD$
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SHA1 (microbiomeutil-r20110519.tgz) = 57fb144de76152447abbe3929357ff8bb887b130
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RMD160 (microbiomeutil-r20110519.tgz) = b3ff65fccf53cbfb3020c2071832c2deea9aa800
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SHA512 (microbiomeutil-r20110519.tgz) = 10965fe45739d8c8395c6e15b67a7057c299336bf7498a99ee12cd6ae96d393b9f92a55485b9a8b621ee276bbe61c11299d94fe3c0de88e1b92aeb546a85fc9f
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Size (microbiomeutil-r20110519.tgz) = 133623556 bytes
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20
microbiomeutil/files/modulefile
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20
microbiomeutil/files/modulefile
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#%Module1.0#####################################################################
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##
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## modules modulefile
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##
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## modulefiles/modules. Generated from modules.in by configure.
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##
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proc ModulesHelp { } {
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puts stderr "\tApplication: microbiomeutil r20110519"
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}
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module-whatis "microbiomeutil"
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set version 2011.05.19
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set appsroot /usr/local/microbiomeutil
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prepend-path PATH $appsroot/ChimeraSlayer
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prepend-path PATH $appsroot/NAST-iEr
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prepend-path PATH $appsroot/TreeChopper
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prepend-path PATH $appsroot/WigeoN
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prepend-path PATH $appsroot/AmosCmp16Spipeline
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10
microbiomeutil/patches/patch-NAST-iEr_NAST-iEr.c
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10
microbiomeutil/patches/patch-NAST-iEr_NAST-iEr.c
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$NetBSD$
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--- NAST-iEr/NAST-iEr.c.orig 2015-02-24 16:16:28.667021760 -0600
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+++ NAST-iEr/NAST-iEr.c 2015-02-24 16:16:40.213027838 -0600
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@@ -1,4 +1,5 @@
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#include <stdlib.h>
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+#include <ctype.h>
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#include <stdio.h>
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#include <string.h>
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#include <unistd.h>
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