git: 49a1ada63293 - main - biology/readseq: Read and reformat biosequences, Java command-line version

[Jason W. Bacon]

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=49a1ada63293e4c27a396fb8997a238dd090e7de

commit 49a1ada63293e4c27a396fb8997a238dd090e7de
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-04-18 13:52:41 +0000
Commit:     Jason W. Bacon <jwb at FreeBSD.org>
CommitDate: 2021-04-18 13:53:02 +0000

    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.
---
 biology/Makefile                 |  1 +
 biology/readseq/Makefile         | 26 ++++++++++++++++++++++++++
 biology/readseq/distinfo         |  3 +++
 biology/readseq/files/readseq.in |  3 +++
 biology/readseq/pkg-descr        |  5 +++++
 5 files changed, 38 insertions(+)

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 at 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