diff options
| -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 |