diff --git a/biology/Makefile b/biology/Makefile index 6712e8a40155..821cf358e8c3 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,230 +1,231 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bamutil SUBDIR += bbmap SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bfc SUBDIR += bio-mocha SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc SUBDIR += biolibc-tools SUBDIR += bioparser SUBDIR += biosig 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 += erminej SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp + SUBDIR += fastq-trim SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += flash SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += generand SUBDIR += gff2ps SUBDIR += gffread 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 += libgff SUBDIR += libgtextutils SUBDIR += libneurosim SUBDIR += libnuml SUBDIR += libsbml SUBDIR += libsedml 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-PySCeS SUBDIR += py-bcbio-gff SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-crossmap SUBDIR += py-cutadapt SUBDIR += py-deeptools SUBDIR += py-deeptoolsintervals SUBDIR += py-dna-features-viewer SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-gffutils SUBDIR += py-goatools SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-libnuml SUBDIR += py-libsedml SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-ont-fast5-api SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-py2bit SUBDIR += py-pybigwig SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-python-libsbml SUBDIR += py-pywgsim 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 += sam2pairwise SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqan3 SUBDIR += seqio SUBDIR += seqkit SUBDIR += seqtk SUBDIR += sigviewer 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/fastq-trim/Makefile b/biology/fastq-trim/Makefile new file mode 100644 index 000000000000..7b10097826ba --- /dev/null +++ b/biology/fastq-trim/Makefile @@ -0,0 +1,22 @@ +PORTNAME= fastq-trim +DISTVERSION= 0.1.1 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Lightening fast sequence read trimmer + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libbiolibc.so:biology/biolibc libxtend.so:devel/libxtend + +USE_GITHUB= yes + +GH_ACCOUNT= outpaddling + +MAKE_ENV= VERSION=${PORTVERSION} + +pre-build: + (cd ${WRKSRC} && ${MAKE} LOCALBASE=${LOCALBASE} depend) + +.include diff --git a/biology/fastq-trim/distinfo b/biology/fastq-trim/distinfo new file mode 100644 index 000000000000..8b2366479432 --- /dev/null +++ b/biology/fastq-trim/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1647691961 +SHA256 (outpaddling-fastq-trim-0.1.1_GH0.tar.gz) = ce959484b823f20a5e6e3c493490e71183865d15b6023ee7dc3a5822cc6b176c +SIZE (outpaddling-fastq-trim-0.1.1_GH0.tar.gz) = 30087 diff --git a/biology/fastq-trim/pkg-descr b/biology/fastq-trim/pkg-descr new file mode 100644 index 000000000000..e3ec0de0561a --- /dev/null +++ b/biology/fastq-trim/pkg-descr @@ -0,0 +1,4 @@ +Fastq-trim is a hopefully lightening fast read trimming tool for QA of +DNA and RNA reads prior to analyses such as RNA-Seq. + +WWW: https://github.com/outpaddling/Fastq-trim diff --git a/biology/fastq-trim/pkg-plist b/biology/fastq-trim/pkg-plist new file mode 100644 index 000000000000..4c55bfdd58f8 --- /dev/null +++ b/biology/fastq-trim/pkg-plist @@ -0,0 +1,75 @@ +bin/fastq-trim +bin/fastq-vis +include/fastq-trim-accessors.h +include/fastq-trim-mutators.h +include/fastq-trim-rvs.h +include/fastq-trim.h +lib/libfastq-trim.a +man/man1/fastq-trim.1.gz +man/man1/fastq-vis.1.gz +man/man3/FASTQ_TRIM_ADAPTER1.3.gz +man/man3/FASTQ_TRIM_ADAPTER1_AE.3.gz +man/man3/FASTQ_TRIM_ADAPTER2.3.gz +man/man3/FASTQ_TRIM_ADAPTER2_AE.3.gz +man/man3/FASTQ_TRIM_ADAPTER_MATCH_FUNCTION.3.gz +man/man3/FASTQ_TRIM_INFILE1.3.gz +man/man3/FASTQ_TRIM_INFILE1_AE.3.gz +man/man3/FASTQ_TRIM_INFILE2.3.gz +man/man3/FASTQ_TRIM_INFILE2_AE.3.gz +man/man3/FASTQ_TRIM_INSTREAM1.3.gz +man/man3/FASTQ_TRIM_INSTREAM1_AE.3.gz +man/man3/FASTQ_TRIM_INSTREAM2.3.gz +man/man3/FASTQ_TRIM_INSTREAM2_AE.3.gz +man/man3/FASTQ_TRIM_MAX_MISMATCH_PERCENT.3.gz +man/man3/FASTQ_TRIM_MIN_LENGTH.3.gz +man/man3/FASTQ_TRIM_MIN_MATCH.3.gz +man/man3/FASTQ_TRIM_MIN_QUAL.3.gz +man/man3/FASTQ_TRIM_OUTFILE1.3.gz +man/man3/FASTQ_TRIM_OUTFILE1_AE.3.gz +man/man3/FASTQ_TRIM_OUTFILE2.3.gz +man/man3/FASTQ_TRIM_OUTFILE2_AE.3.gz +man/man3/FASTQ_TRIM_OUTSTREAM1.3.gz +man/man3/FASTQ_TRIM_OUTSTREAM1_AE.3.gz +man/man3/FASTQ_TRIM_OUTSTREAM2.3.gz +man/man3/FASTQ_TRIM_OUTSTREAM2_AE.3.gz +man/man3/FASTQ_TRIM_PHRED_BASE.3.gz +man/man3/FASTQ_TRIM_POLYA_MIN_LEN.3.gz +man/man3/FASTQ_TRIM_VERBOSE.3.gz +man/man3/fastq_trim_set_adapter1.3.gz +man/man3/fastq_trim_set_adapter1_ae.3.gz +man/man3/fastq_trim_set_adapter1_cpy.3.gz +man/man3/fastq_trim_set_adapter2.3.gz +man/man3/fastq_trim_set_adapter2_ae.3.gz +man/man3/fastq_trim_set_adapter2_cpy.3.gz +man/man3/fastq_trim_set_adapter_match_function.3.gz +man/man3/fastq_trim_set_infile1.3.gz +man/man3/fastq_trim_set_infile1_ae.3.gz +man/man3/fastq_trim_set_infile1_cpy.3.gz +man/man3/fastq_trim_set_infile2.3.gz +man/man3/fastq_trim_set_infile2_ae.3.gz +man/man3/fastq_trim_set_infile2_cpy.3.gz +man/man3/fastq_trim_set_instream1.3.gz +man/man3/fastq_trim_set_instream1_ae.3.gz +man/man3/fastq_trim_set_instream1_cpy.3.gz +man/man3/fastq_trim_set_instream2.3.gz +man/man3/fastq_trim_set_instream2_ae.3.gz +man/man3/fastq_trim_set_instream2_cpy.3.gz +man/man3/fastq_trim_set_max_mismatch_percent.3.gz +man/man3/fastq_trim_set_min_length.3.gz +man/man3/fastq_trim_set_min_match.3.gz +man/man3/fastq_trim_set_min_qual.3.gz +man/man3/fastq_trim_set_outfile1.3.gz +man/man3/fastq_trim_set_outfile1_ae.3.gz +man/man3/fastq_trim_set_outfile1_cpy.3.gz +man/man3/fastq_trim_set_outfile2.3.gz +man/man3/fastq_trim_set_outfile2_ae.3.gz +man/man3/fastq_trim_set_outfile2_cpy.3.gz +man/man3/fastq_trim_set_outstream1.3.gz +man/man3/fastq_trim_set_outstream1_ae.3.gz +man/man3/fastq_trim_set_outstream1_cpy.3.gz +man/man3/fastq_trim_set_outstream2.3.gz +man/man3/fastq_trim_set_outstream2_ae.3.gz +man/man3/fastq_trim_set_outstream2_cpy.3.gz +man/man3/fastq_trim_set_phred_base.3.gz +man/man3/fastq_trim_set_polya_min_len.3.gz +man/man3/fastq_trim_set_verbose.3.gz