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 + +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 ++#include + #include + #include + #include