diff --git a/biology/Makefile b/biology/Makefile index 158eb70ede1a..55ed6b8c2735 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,203 +1,204 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bbmap SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc SUBDIR += bioparser SUBDIR += biosoup SUBDIR += biostar-tools SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += edlib 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 += gcta SUBDIR += gemma SUBDIR += generand SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += groopm SUBDIR += haplohseq 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 += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 + SUBDIR += mmseqs2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-entrez-direct SUBDIR += ncbi-toolkit SUBDIR += ncbi-vdb SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-DB-EMBL SUBDIR += p5-Bio-DB-NCBIHelper 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-Bio-Variation SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbseqan SUBDIR += peak-classifier SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phyml SUBDIR += picard-tools SUBDIR += plink SUBDIR += pooler SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-bigwig SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-crossmap SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-resdk SUBDIR += py-scikit-bio SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += rampler SUBDIR += readseq SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += rubygem-bio-executables SUBDIR += rubygem-bio-old-biofetch-emulator SUBDIR += rubygem-bio-shell SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqan3 SUBDIR += seqio SUBDIR += seqkit SUBDIR += seqtk SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += snpeff SUBDIR += spoa SUBDIR += sra-tools SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += taxonkit SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ucsc-userapps SUBDIR += ugene SUBDIR += unikmer SUBDIR += vcf-split SUBDIR += vcf2hap SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt SUBDIR += wise .include diff --git a/biology/mmseqs2/Makefile b/biology/mmseqs2/Makefile new file mode 100644 index 000000000000..6ec07e428c72 --- /dev/null +++ b/biology/mmseqs2/Makefile @@ -0,0 +1,27 @@ +PORTNAME= MMseqs2 +DISTVERSION= 13-45111 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Ultra fast and sensitive sequence search and clustering suite + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE.md + +USES= cmake perl5 shebangfix + +SHEBANG_GLOB= *.sh + +USE_GITHUB= yes +GH_ACCOUNT= soedinglab + +PLIST_FILES= bin/mmseqs ${DATADIR}/bash-completion.sh + +post-patch: + @${REINPLACE_CMD} -e 's|MMSEQS_HOME/util|${DATADIR}|g' \ + ${WRKSRC}/src/commons/Application.cpp + +post-stage: + ${MV} ${STAGEDIR}${PREFIX}/util ${STAGEDIR}${DATADIR} + +.include diff --git a/biology/mmseqs2/distinfo b/biology/mmseqs2/distinfo new file mode 100644 index 000000000000..ec7fbc69cf89 --- /dev/null +++ b/biology/mmseqs2/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1624543564 +SHA256 (soedinglab-MMseqs2-13-45111_GH0.tar.gz) = 6444bb682ebf5ced54b2eda7a301fa3e933c2a28b7661f96ef5bdab1d53695a2 +SIZE (soedinglab-MMseqs2-13-45111_GH0.tar.gz) = 10196433 diff --git a/biology/mmseqs2/files/patch-CMakeLists.txt b/biology/mmseqs2/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..908984972649 --- /dev/null +++ b/biology/mmseqs2/files/patch-CMakeLists.txt @@ -0,0 +1,53 @@ +--- CMakeLists.txt.orig 2021-06-24 14:37:49 UTC ++++ CMakeLists.txt +@@ -50,30 +50,19 @@ set(MMSEQS_CXX_FLAGS "-fsigned-char") + # SIMD instruction sets support + set(MMSEQS_ARCH "") + if (HAVE_AVX2) +- if (CMAKE_COMPILER_IS_CLANG) +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -mavx2 -mcx16") +- else () +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -mavx2 -mcx16 -Wa,-q") +- endif () + set(X64 1) + elseif (HAVE_SSE4_1) +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -msse4.1 -mcx16") + set(X64 1) + elseif (HAVE_SSE2) +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -msse2") + set(DISABLE_IPS4O 1) + set(X64 1) + elseif (HAVE_POWER9) +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -mcpu=power9 -mvsx") + set(PPC64 1) + elseif (HAVE_POWER8) +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -mcpu=power8 -mvsx") + set(PPC64 1) + elseif (HAVE_ARM8) +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -march=armv8-a+simd") + set(ARM 1) + elseif (HAVE_S390X) +- set(MMSEQS_ARCH "${MMSEQS_ARCH} -mzarch -march=z14") + set(ZARCH 1) + endif () + +@@ -105,19 +94,6 @@ if (NATIVE_ARCH AND (MMSEQS_ARCH STREQUAL "")) + endif () + if (PPC64) + set(MMSEQS_ARCH "-mcpu=native") +- else () +- # clang has a problem with march=native on travis +- if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS "4.0.0") +- set(MMSEQS_ARCH "${SSE_FLAGS}") +- else() +- set(MMSEQS_ARCH "-march=native") +- endif() +- endif () +- else () +- if (PPC64) +- set(MMSEQS_ARCH "-mcpu=native") +- else () +- set(MMSEQS_ARCH "-march=native") + endif () + endif () + endif () diff --git a/biology/mmseqs2/pkg-descr b/biology/mmseqs2/pkg-descr new file mode 100644 index 000000000000..128056f15f39 --- /dev/null +++ b/biology/mmseqs2/pkg-descr @@ -0,0 +1,10 @@ +MMseqs2 (Many-against-Many sequence searching) is a software suite to search +and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source +GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta +version, via cygwin) Windows. The software is designed to run on multiple cores +and servers and exhibits very good scalability. MMseqs2 can run 10000 times +faster than BLAST. At 100 times its speed it achieves almost the same +sensitivity. It can perform profile searches with the same sensitivity as +PSI-BLAST at over 400 times its speed. + +WWW: https://github.com/soedinglab/MMseqs2