Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 502014) +++ head/biology/Makefile (revision 502015) @@ -1,165 +1,166 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += consed SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gemma SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm + SUBDIR += hhsuite SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-xenaPython SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += vsearch SUBDIR += wise .include Index: head/biology/hhsuite/Makefile =================================================================== --- head/biology/hhsuite/Makefile (nonexistent) +++ head/biology/hhsuite/Makefile (revision 502015) @@ -0,0 +1,26 @@ +# $FreeBSD$ + +PORTNAME= hhsuite +DISTVERSIONPREFIX= v +DISTVERSION= 3.2.0 +CATEGORIES= biology science + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Remote protein homology detection suite + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= openmpi>0:net/openmpi +LIB_DEPENDS= libomp.so:devel/openmp +RUN_DEPENDS= openmpi>0:net/openmpi + +USES= cmake perl5 python shebangfix +SHEBANG_GLOB= *.pl *.py +USE_GITHUB= yes +GH_ACCOUNT= soedinglab +GH_PROJECT= hh-suite + +LDFLAGS+= -Wl,-rpath,${LOCALBASE}/mpi/openmpi/lib -L${LOCALBASE}/mpi/openmpi/lib -lmpi # force linking to openmpi, and not to mpich + +.include Property changes on: head/biology/hhsuite/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/hhsuite/distinfo =================================================================== --- head/biology/hhsuite/distinfo (nonexistent) +++ head/biology/hhsuite/distinfo (revision 502015) @@ -0,0 +1,3 @@ +TIMESTAMP = 1558244086 +SHA256 (soedinglab-hh-suite-v3.2.0_GH0.tar.gz) = 6b870dcfbc1ffb9dd664a45415fcd13cf5970f49d1c7b824160c260fa138e6d6 +SIZE (soedinglab-hh-suite-v3.2.0_GH0.tar.gz) = 6273589 Property changes on: head/biology/hhsuite/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/hhsuite/files/patch-data_CMakeLists.txt =================================================================== --- head/biology/hhsuite/files/patch-data_CMakeLists.txt (nonexistent) +++ head/biology/hhsuite/files/patch-data_CMakeLists.txt (revision 502015) @@ -0,0 +1,11 @@ +--- data/CMakeLists.txt.orig 2019-05-19 05:46:02 UTC ++++ data/CMakeLists.txt +@@ -7,7 +7,7 @@ INSTALL(FILES + do_not_delete.pin + do_not_delete.psq + PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ +- DESTINATION data ++ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/hhsuite/data + ) + + include(ResourceCompiler) Property changes on: head/biology/hhsuite/files/patch-data_CMakeLists.txt ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/hhsuite/files/patch-scripts_CMakeLists.txt =================================================================== --- head/biology/hhsuite/files/patch-scripts_CMakeLists.txt (nonexistent) +++ head/biology/hhsuite/files/patch-scripts_CMakeLists.txt (revision 502015) @@ -0,0 +1,9 @@ +--- scripts/CMakeLists.txt.orig 2019-05-19 05:44:58 UTC ++++ scripts/CMakeLists.txt +@@ -21,5 +21,5 @@ INSTALL(PROGRAMS + reformat.pl + renumberpdb.pl + splitfasta.pl +- DESTINATION scripts ++ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/hhsuite/scripts + ) Property changes on: head/biology/hhsuite/files/patch-scripts_CMakeLists.txt ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/hhsuite/files/patch-src_cs_getopt__pp.cc =================================================================== --- head/biology/hhsuite/files/patch-src_cs_getopt__pp.cc (nonexistent) +++ head/biology/hhsuite/files/patch-src_cs_getopt__pp.cc (revision 502015) @@ -0,0 +1,11 @@ +--- src/cs/getopt_pp.cc.orig 2019-05-19 05:36:03 UTC ++++ src/cs/getopt_pp.cc +@@ -21,7 +21,7 @@ + #include + #include "getopt_pp.h" + +-#ifdef __APPLE__ ++#if defined(__APPLE__) || defined(__FreeBSD__) + extern char** environ; + #endif + Property changes on: head/biology/hhsuite/files/patch-src_cs_getopt__pp.cc ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/hhsuite/pkg-descr =================================================================== --- head/biology/hhsuite/pkg-descr (nonexistent) +++ head/biology/hhsuite/pkg-descr (revision 502015) @@ -0,0 +1,8 @@ +SIMD-vectorized implementation of the Viterbi algorithm for profile HMM +alignment and introduced various other speed-ups. This accelerated HHsearch by a +factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is +~10x faster than PSI-BLAST and ~20x faster than HMMER3. Jobs to perform HHsearch +and HHblits searches with many query profile HMMs can be parallelized over cores +and over servers in a cluster using OpenMP and message passing interface (MPI). + +WWW: https://github.com/soedinglab/hh-suite Property changes on: head/biology/hhsuite/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/hhsuite/pkg-plist =================================================================== --- head/biology/hhsuite/pkg-plist (nonexistent) +++ head/biology/hhsuite/pkg-plist (revision 502015) @@ -0,0 +1,59 @@ +bin/a3m_database_extract +bin/a3m_database_filter +bin/a3m_database_reduce +bin/a3m_extract +bin/a3m_reduce +bin/cstranslate +bin/cstranslate_mpi +bin/ffindex_apply +bin/ffindex_apply_mpi +bin/ffindex_build +bin/ffindex_from_fasta +bin/ffindex_from_fasta_with_split +bin/ffindex_get +bin/ffindex_modify +bin/ffindex_order +bin/ffindex_reduce +bin/ffindex_unpack +bin/hhalign +bin/hhalign_mpi +bin/hhalign_omp +bin/hhblits +bin/hhblits_ca3m +bin/hhblits_mpi +bin/hhblits_omp +bin/hhconsensus +bin/hhfilter +bin/hhmake +bin/hhsearch +bin/hhsearch_mpi +bin/hhsearch_omp +%%DATADIR%%/data/context_data.crf +%%DATADIR%%/data/context_data.lib +%%DATADIR%%/data/cs219.lib +%%DATADIR%%/data/do_not_delete +%%DATADIR%%/data/do_not_delete.phr +%%DATADIR%%/data/do_not_delete.pin +%%DATADIR%%/data/do_not_delete.psq +%%DATADIR%%/scripts/Align.pm +%%DATADIR%%/scripts/HHPaths.pm +%%DATADIR%%/scripts/a3m.py +%%DATADIR%%/scripts/addss.pl +%%DATADIR%%/scripts/check_a3m.py +%%DATADIR%%/scripts/cif2fasta.py +%%DATADIR%%/scripts/create_profile_from_hhm.pl +%%DATADIR%%/scripts/create_profile_from_hmmer.pl +%%DATADIR%%/scripts/ffindex.py +%%DATADIR%%/scripts/get_a3m_size.py +%%DATADIR%%/scripts/hh_reader.py +%%DATADIR%%/scripts/hhmakemodel.pl +%%DATADIR%%/scripts/hhmakemodel.py +%%DATADIR%%/scripts/hhsuitedb.py +%%DATADIR%%/scripts/mergeali.pl +%%DATADIR%%/scripts/multithread.pl +%%DATADIR%%/scripts/pdb2fasta.pl +%%DATADIR%%/scripts/pdbfilter.pl +%%DATADIR%%/scripts/pdbfilter.py +%%DATADIR%%/scripts/reformat.pl +%%DATADIR%%/scripts/renumberpdb.pl +%%DATADIR%%/scripts/splitfasta.pl Property changes on: head/biology/hhsuite/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property