svn commit: r470575 - in head/biology: . clustalx clustalx/files
Jason W. Bacon
jwb at FreeBSD.org
Mon May 21 20:56:20 UTC 2018
Author: jwb
Date: Mon May 21 20:56:17 2018
New Revision: 470575
URL: https://svnweb.freebsd.org/changeset/ports/470575
Log:
biology/clustalx: Multiple alignment of nucleic acid and protein sequences with GUI
Approved by: jrm
Differential Revision: https://reviews.freebsd.org/D15505
Added:
head/biology/clustalx/
head/biology/clustalx/Makefile (contents, props changed)
head/biology/clustalx/distinfo (contents, props changed)
head/biology/clustalx/files/
head/biology/clustalx/files/patch-clustalW_general_VectorOutOfRange.h (contents, props changed)
head/biology/clustalx/pkg-descr (contents, props changed)
Modified:
head/biology/Makefile
Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile Mon May 21 20:39:16 2018 (r470574)
+++ head/biology/Makefile Mon May 21 20:56:17 2018 (r470575)
@@ -20,6 +20,7 @@
SUBDIR += cdbfasta
SUBDIR += chemeq
SUBDIR += clustalw
+ SUBDIR += clustalx
SUBDIR += consed
SUBDIR += crux
SUBDIR += ddocent
Added: head/biology/clustalx/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/clustalx/Makefile Mon May 21 20:56:17 2018 (r470575)
@@ -0,0 +1,36 @@
+# $FreeBSD$
+
+PORTNAME= clustalx
+DISTVERSION= 2.1
+CATEGORIES= biology
+MASTER_SITES= http://www.clustal.org/download/current/ \
+ ftp://ftp.ebi.ac.uk/pub/software/clustalw2/${DISTVERSION}/
+
+MAINTAINER= jwb at FreeBSD.org
+COMMENT= Multiple alignment of nucleic acid and protein sequences with GUI
+
+LICENSE= LGPL3
+LICENSE_FILE= ${WRKSRC}/COPYING
+
+USES= qmake
+USE_QT4= corelib gui moc qmake_build xml
+
+PLIST_FILES= bin/clustalx \
+ ${DATADIR}/colprot.xml \
+ ${DATADIR}/coldna.xml \
+ ${DATADIR}/colprint.xml \
+ ${DATADIR}/clustalx.hlp
+
+post-patch:
+ @${REINPLACE_CMD} -e 's|col.*.xml|${DATADIR}/&|' \
+ ${WRKSRC}/ClustalQtParams.h
+ @${REINPLACE_CMD} -e 's|clustalx.hlp|${DATADIR}/&|' \
+ ${WRKSRC}/HelpDisplayWidget.cpp
+
+do-install:
+ ${INSTALL_PROGRAM} ${WRKSRC}/clustalx ${STAGEDIR}${PREFIX}/bin
+ @${MKDIR} ${STAGEDIR}${DATADIR}
+ ${INSTALL_DATA} ${WRKSRC}/col*.xml ${WRKSRC}/clustalx.hlp \
+ ${STAGEDIR}${DATADIR}
+
+.include <bsd.port.mk>
Added: head/biology/clustalx/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/clustalx/distinfo Mon May 21 20:56:17 2018 (r470575)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1526839706
+SHA256 (clustalx-2.1.tar.gz) = e10adb728c320598a165ca529f1aa3d2560061de0236e0a0926eaca9554afa05
+SIZE (clustalx-2.1.tar.gz) = 341649
Added: head/biology/clustalx/files/patch-clustalW_general_VectorOutOfRange.h
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/clustalx/files/patch-clustalW_general_VectorOutOfRange.h Mon May 21 20:56:17 2018 (r470575)
@@ -0,0 +1,11 @@
+--- clustalW/general/VectorOutOfRange.h.orig 2018-05-20 18:08:08 UTC
++++ clustalW/general/VectorOutOfRange.h
+@@ -5,6 +5,8 @@
+ */
+ #include <stdexcept>
+ #include <exception>
++#include <string>
++
+ namespace clustalw
+ {
+
Added: head/biology/clustalx/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/clustalx/pkg-descr Mon May 21 20:56:17 2018 (r470575)
@@ -0,0 +1,8 @@
+ClustalX is the graphical version of Clustal, a general purpose multiple
+sequence alignment program for DNA or proteins. It produces biologically
+meaningful multiple sequence alignments of divergent sequences. It calculates
+the best match for the selected sequences, and lines them up so that the
+identities, similarities and differences can be seen. Evolutionary
+relationships can be seen via viewing Cladograms or Phylograms.
+
+WWW: http://www.clustal.org/
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