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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-04-18 13:52:41 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-04-18 13:53:02 +0000 |
| commit | 49a1ada63293e4c27a396fb8997a238dd090e7de (patch) | |
| tree | 3a8f1daf7d92a5cefee5d7f5d672ac0c4528cbb4 /biology | |
| parent | 1dddbd517339425d59febc4cde1b037958e92920 (diff) | |
| download | ports-49a1ada63293e4c27a396fb8997a238dd090e7de.tar.gz ports-49a1ada63293e4c27a396fb8997a238dd090e7de.zip | |
biology/readseq: Read and reformat biosequences, Java command-line version
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.
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/readseq/Makefile | 26 | ||||
| -rw-r--r-- | biology/readseq/distinfo | 3 | ||||
| -rwxr-xr-x | biology/readseq/files/readseq.in | 3 | ||||
| -rw-r--r-- | biology/readseq/pkg-descr | 5 |
5 files changed, 38 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index adb71952bb1e..956405f7e693 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -148,6 +148,7 @@ SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += rampler + SUBDIR += readseq SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio 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 <bsd.port.mk> 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 |