Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 455153) +++ head/biology/Makefile (revision 455154) @@ -1,116 +1,117 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += ariadne SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustalw SUBDIR += consed SUBDIR += crux SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-toolkit SUBDIR += njplot SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene 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-transdecoder SUBDIR += paml SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plink SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python + SUBDIR += py-cutadapt SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += ssaha SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/py-cutadapt/Makefile =================================================================== --- head/biology/py-cutadapt/Makefile (nonexistent) +++ head/biology/py-cutadapt/Makefile (revision 455154) @@ -0,0 +1,23 @@ +# $FreeBSD$ + +PORTNAME= cutadapt +PORTVERSION= 1.14 +CATEGORIES= biology python +MASTER_SITES= CHEESESHOP +MASTER_SITE_SUBDIR= source/c/cutadapt +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Finds and removes adapter sequences, primers, poly-A tails, etc + +LICENSE= MIT + +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}xopen>0:archivers/py-xopen + +USES= python +USE_PYTHON= distutils + +post-install: + @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/cutadapt/*.so + +.include Property changes on: head/biology/py-cutadapt/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/py-cutadapt/distinfo =================================================================== --- head/biology/py-cutadapt/distinfo (nonexistent) +++ head/biology/py-cutadapt/distinfo (revision 455154) @@ -0,0 +1,3 @@ +TIMESTAMP = 1509552013 +SHA256 (cutadapt-1.14.tar.gz) = f32990a8b2f8b53f8f4c723ada3d256a8e8476febdd296506764cc8e83397d3d +SIZE (cutadapt-1.14.tar.gz) = 283631 Property changes on: head/biology/py-cutadapt/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ 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/py-cutadapt/pkg-descr =================================================================== --- head/biology/py-cutadapt/pkg-descr (nonexistent) +++ head/biology/py-cutadapt/pkg-descr (revision 455154) @@ -0,0 +1,4 @@ +Cutadapt finds and removes adapter sequences, primers, poly-A tails and other +types of unwanted sequences from your high-throughput sequencing reads. + +WWW: https://pypi.python.org/pypi/cutadapt/ Property changes on: head/biology/py-cutadapt/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ 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/py-cutadapt/pkg-plist =================================================================== --- head/biology/py-cutadapt/pkg-plist (nonexistent) +++ head/biology/py-cutadapt/pkg-plist (revision 455154) @@ -0,0 +1,43 @@ +bin/cutadapt +%%PYTHON_SITELIBDIR%%/cutadapt/__init__.py +%%PYTHON_SITELIBDIR%%/cutadapt/__init__.pyc +%%PYTHON_SITELIBDIR%%/cutadapt/__init__.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/cutadapt/_align.so +%%PYTHON_SITELIBDIR%%/cutadapt/_qualtrim.so +%%PYTHON_SITELIBDIR%%/cutadapt/_seqio.so +%%PYTHON_SITELIBDIR%%/cutadapt/_version.py +%%PYTHON_SITELIBDIR%%/cutadapt/_version.pyc +%%PYTHON_SITELIBDIR%%/cutadapt/_version.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/cutadapt/adapters.py +%%PYTHON_SITELIBDIR%%/cutadapt/adapters.pyc +%%PYTHON_SITELIBDIR%%/cutadapt/adapters.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/cutadapt/align.py +%%PYTHON_SITELIBDIR%%/cutadapt/align.pyc +%%PYTHON_SITELIBDIR%%/cutadapt/align.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/cutadapt/colorspace.py +%%PYTHON_SITELIBDIR%%/cutadapt/colorspace.pyc +%%PYTHON_SITELIBDIR%%/cutadapt/colorspace.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/cutadapt/compat.py +%%PYTHON_SITELIBDIR%%/cutadapt/compat.pyc +%%PYTHON_SITELIBDIR%%/cutadapt/compat.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/cutadapt/filters.py +%%PYTHON_SITELIBDIR%%/cutadapt/filters.pyc +%%PYTHON_SITELIBDIR%%/cutadapt/filters.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/cutadapt/modifiers.py +%%PYTHON_SITELIBDIR%%/cutadapt/modifiers.pyc +%%PYTHON_SITELIBDIR%%/cutadapt/modifiers.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/cutadapt/qualtrim.py +%%PYTHON_SITELIBDIR%%/cutadapt/qualtrim.pyc +%%PYTHON_SITELIBDIR%%/cutadapt/qualtrim.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/cutadapt/report.py +%%PYTHON_SITELIBDIR%%/cutadapt/report.pyc +%%PYTHON_SITELIBDIR%%/cutadapt/report.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/cutadapt/scripts/__init__.py +%%PYTHON_SITELIBDIR%%/cutadapt/scripts/__init__.pyc +%%PYTHON_SITELIBDIR%%/cutadapt/scripts/__init__.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/cutadapt/scripts/cutadapt.py +%%PYTHON_SITELIBDIR%%/cutadapt/scripts/cutadapt.pyc +%%PYTHON_SITELIBDIR%%/cutadapt/scripts/cutadapt.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/cutadapt/seqio.py +%%PYTHON_SITELIBDIR%%/cutadapt/seqio.pyc +%%PYTHON_SITELIBDIR%%/cutadapt/seqio.%%PYTHON_PYOEXTENSION%% Property changes on: head/biology/py-cutadapt/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ 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