diff --git a/biology/Makefile b/biology/Makefile index adb71952bb1e..956405f7e693 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,191 +1,192 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc SUBDIR += bioparser SUBDIR += biosoup 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 += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit 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 += 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-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 += seqio SUBDIR += seqkit SUBDIR += seqtk SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += spoa SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcf-split SUBDIR += vcf2hap SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt SUBDIR += wise .include diff --git a/biology/readseq/Makefile b/biology/readseq/Makefile new file mode 100644 index 000000000000..5956dbea4551 --- /dev/null +++ b/biology/readseq/Makefile @@ -0,0 +1,26 @@ +# $FreeBSD$ + +PORTNAME= readseq +DISTVERSION= 2.1.19 +CATEGORIES= biology java +# The site used by bioconda for 2.1.30 is down as of 2021-04-13 +# MASTER_SITES= http://iubio.bio.indiana.edu/soft/molbio/readseq/java/ +MASTER_SITES= https://sourceforge.net/projects/readseq/files/latest/ +DISTNAME= ${PORTNAME} +EXTRACT_SUFX= .jar + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Read and reformat biosequences, Java command-line version + +LICENSE= PD + +USE_JAVA= yes +NO_BUILD= yes +SUB_FILES= readseq +PLIST_FILES= bin/readseq share/java/classes/readseq.jar + +do-install: + ${INSTALL_DATA} ${DISTDIR}/${DISTFILES} ${STAGEDIR}${JAVAJARDIR} + ${INSTALL_SCRIPT} ${WRKDIR}/readseq ${STAGEDIR}${PREFIX}/bin + +.include diff --git a/biology/readseq/distinfo b/biology/readseq/distinfo new file mode 100644 index 000000000000..a4a40484d345 --- /dev/null +++ b/biology/readseq/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1618350447 +SHA256 (readseq.jar) = 966e7d4e1c4c6add588b3ead281c993c6a0c35b991a1ded53f81230a54ac6778 +SIZE (readseq.jar) = 767702 diff --git a/biology/readseq/files/readseq.in b/biology/readseq/files/readseq.in new file mode 100755 index 000000000000..41d8d2466c57 --- /dev/null +++ b/biology/readseq/files/readseq.in @@ -0,0 +1,3 @@ +#!/bin/sh -e + +java -jar %%JAVAJARDIR%%/readseq.jar "$@" diff --git a/biology/readseq/pkg-descr b/biology/readseq/pkg-descr new file mode 100644 index 000000000000..f07d55783e38 --- /dev/null +++ b/biology/readseq/pkg-descr @@ -0,0 +1,5 @@ +Sequence reading library developed by the Ribosomal Database Project. It can +handle genbank, embl, fasta, fastq, sff and sto files, can read from files or +streams, and can handle indexing files. + +WWW: https://sourceforge.net/projects/readseq