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freebsd-ports/biology/emboss/Makefile

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- Reassign to the heap at maintainer's request
2012-10-01 16:45:16 +02:00
# Created by: Johann Visagie <johann@egenetics.com>
Add emboss, the European Molecular Biology Open Software Suite PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com>
2000-07-31 21:13:54 +02:00
# $FreeBSD$
PORTNAME= emboss
- Update to 6.2.0 Submitted by: Wen Heping(myself) Approved by: maintainer(via Email)
2010-04-07 03:21:36 +02:00
PORTVERSION= 6.2.0
- Update to 5.0.0 PR: ports/122437 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
2008-04-13 09:22:42 +02:00
RELEASE= ${PORTNAME:U}-${PORTVERSION}
- update libdg to 2.1.0
2013-08-09 16:05:52 +02:00
PORTREVISION= 3
Add emboss, the European Molecular Biology Open Software Suite PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com>
2000-07-31 21:13:54 +02:00
CATEGORIES= biology
- Update to 6.2.0 Submitted by: Wen Heping(myself) Approved by: maintainer(via Email)
2010-04-07 03:21:36 +02:00
MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/
- Update to 5.0.0 PR: ports/122437 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
2008-04-13 09:22:42 +02:00
DISTNAME= ${RELEASE}
For EMBOSS: This patch brings EMBOSS up to date with the current version. i. The patches included in files/ are bugfixes for files in EMBOSS-3.0.0 that appeared after the release. They are documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README This is just 'for the record' so that we remember to remove these patches in the next update. ii. EMBOSS is now installed by default in LOCALBASE/emboss This is to avoid CONFLICTS with other ports that install files with the same names. Installing EMBOSS to another PREFIX is also possible. iii. now EMBASSY and EMBOSS both store their distfiles in the same DIST_SUBDIR iv. use built-in PKGMESSAGE and SUB_FILES instead of doing it the old (manual) way For EMBASSY: This update brings embassy in sync with the update of EMBOSS to 3.0.0. Things that changed from previous version of the port: i. embassy now installs by default in $LOCALBASE/emboss (the new default PREFIX for emboss as well). ii. changed DIST_SUBDIR so that all the distfiles are put together with emboss. This makes sense(TM) iii. incorporated new EMBASSY apps (this accounts for the changes in OPTIONS and pkg-plist) iv. removed obsoleted patches Finally, I included a sample text that could go in UPDATING. PR: 93053 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)
2006-03-31 11:43:21 +02:00
DIST_SUBDIR= ${PORTNAME}
Add emboss, the European Molecular Biology Open Software Suite PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com>
2000-07-31 21:13:54 +02:00
- Take maintainership
2012-10-01 16:55:55 +02:00
MAINTAINER= wen@FreeBSD.org
Clear moonlight beckons. Requiem mors pacem pkg-comment, And be calm ports tree. E Nomini Patri, E Fili, E Spiritu Sancti.
2003-03-07 07:14:21 +01:00
COMMENT= A collection of open source tools for genetic sequence analysis
Add emboss, the European Molecular Biology Open Software Suite PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com>
2000-07-31 21:13:54 +02:00
- Update to 2.9.0 - Pass maintainership to submitter PR: ports/74333 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar>
2004-11-26 02:11:43 +01:00
BUILD_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw \
primer3:${PORTSDIR}/biology/primer3
In preparation for making libtool generate libraries with a sane name, fix all LIB_DEPENDS in biology
2013-12-11 15:43:51 +01:00
LIB_DEPENDS= libgd.so:${PORTSDIR}/graphics/gd \
libpng15.so:${PORTSDIR}/graphics/png
Add emboss, the European Molecular Biology Open Software Suite PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com>
2000-07-31 21:13:54 +02:00
For EMBOSS: This patch brings EMBOSS up to date with the current version. i. The patches included in files/ are bugfixes for files in EMBOSS-3.0.0 that appeared after the release. They are documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README This is just 'for the record' so that we remember to remove these patches in the next update. ii. EMBOSS is now installed by default in LOCALBASE/emboss This is to avoid CONFLICTS with other ports that install files with the same names. Installing EMBOSS to another PREFIX is also possible. iii. now EMBASSY and EMBOSS both store their distfiles in the same DIST_SUBDIR iv. use built-in PKGMESSAGE and SUB_FILES instead of doing it the old (manual) way For EMBASSY: This update brings embassy in sync with the update of EMBOSS to 3.0.0. Things that changed from previous version of the port: i. embassy now installs by default in $LOCALBASE/emboss (the new default PREFIX for emboss as well). ii. changed DIST_SUBDIR so that all the distfiles are put together with emboss. This makes sense(TM) iii. incorporated new EMBASSY apps (this accounts for the changes in OPTIONS and pkg-plist) iv. removed obsoleted patches Finally, I included a sample text that could go in UPDATING. PR: 93053 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)
2006-03-31 11:43:21 +02:00
CONFLICTS= qmail-ldap-[0-9]* digest-[0-9]*
- Add (or fix) CONFLICTS line. The ports install bin/digest. Approved by: portmgr (krion)
2005-02-11 22:11:51 +01:00
For EMBOSS: This patch brings EMBOSS up to date with the current version. i. The patches included in files/ are bugfixes for files in EMBOSS-3.0.0 that appeared after the release. They are documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README This is just 'for the record' so that we remember to remove these patches in the next update. ii. EMBOSS is now installed by default in LOCALBASE/emboss This is to avoid CONFLICTS with other ports that install files with the same names. Installing EMBOSS to another PREFIX is also possible. iii. now EMBASSY and EMBOSS both store their distfiles in the same DIST_SUBDIR iv. use built-in PKGMESSAGE and SUB_FILES instead of doing it the old (manual) way For EMBASSY: This update brings embassy in sync with the update of EMBOSS to 3.0.0. Things that changed from previous version of the port: i. embassy now installs by default in $LOCALBASE/emboss (the new default PREFIX for emboss as well). ii. changed DIST_SUBDIR so that all the distfiles are put together with emboss. This makes sense(TM) iii. incorporated new EMBASSY apps (this accounts for the changes in OPTIONS and pkg-plist) iv. removed obsoleted patches Finally, I included a sample text that could go in UPDATING. PR: 93053 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)
2006-03-31 11:43:21 +02:00
PREFIX?= ${LOCALBASE}/emboss
NO_MTREE= yes
Convert from USE_MOTIF to USES=motif While here: - trim headers - Remove indefinite article from comment - convert USE_GMAKE to USES=gmake
2013-07-09 23:49:35 +02:00
USES= gmake
Add USE_SUBMAKE, where it might be necessary.
2002-03-25 10:19:20 +01:00
USE_SUBMAKE= yes
- Update to version 2.2.0 - Update included EMBASSY package EMNU - Fix a long-standing bug in Makefile that would preclude PKGMESSAGE from being generated properly - Consider this an interim update merely to track the latest version - more work is required to activate the newly included "Jemboss" Java GUI interface
2002-01-18 15:04:03 +01:00
GNU_CONFIGURE= yes
Sync to new bsd.autotools.mk
2010-12-04 08:34:27 +01:00
USE_AUTOTOOLS= libtool
- Update to 5.0.0 PR: ports/122437 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
2008-04-13 09:22:42 +02:00
USE_LDCONFIG= yes
For EMBOSS: This patch brings EMBOSS up to date with the current version. i. The patches included in files/ are bugfixes for files in EMBOSS-3.0.0 that appeared after the release. They are documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README This is just 'for the record' so that we remember to remove these patches in the next update. ii. EMBOSS is now installed by default in LOCALBASE/emboss This is to avoid CONFLICTS with other ports that install files with the same names. Installing EMBOSS to another PREFIX is also possible. iii. now EMBASSY and EMBOSS both store their distfiles in the same DIST_SUBDIR iv. use built-in PKGMESSAGE and SUB_FILES instead of doing it the old (manual) way For EMBASSY: This update brings embassy in sync with the update of EMBOSS to 3.0.0. Things that changed from previous version of the port: i. embassy now installs by default in $LOCALBASE/emboss (the new default PREFIX for emboss as well). ii. changed DIST_SUBDIR so that all the distfiles are put together with emboss. This makes sense(TM) iii. incorporated new EMBASSY apps (this accounts for the changes in OPTIONS and pkg-plist) iv. removed obsoleted patches Finally, I included a sample text that could go in UPDATING. PR: 93053 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)
2006-03-31 11:43:21 +02:00
SUB_FILES= pkg-message
SUB_LIST= PREFIX=${PREFIX} DATADIR=${DATADIR}
Make nolonger support :U. Fix to compensate for that. Submitted by: fenner Approved by: MAINTAINER
2000-11-19 04:06:48 +01:00
- Update to 5.0.0 PR: ports/122437 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
2008-04-13 09:22:42 +02:00
DOCSDIR= ${PREFIX}/share/${PORTNAME:U}/doc
- Update to 2.9.0 - Pass maintainership to submitter PR: ports/74333 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar>
2004-11-26 02:11:43 +01:00
DATADIR= ${PREFIX}/share/${PORTNAME:U}
- This is a fairly extensive rework of this port. - "EMBASSY" applications are third party tools which have been adapted to function as part of EMBOSS, but which are not included with the base EMBOSS distribution for licensing or other reasons. This new version of the EMBOSS port now contains the three current EMBASSY applications as well, and during installation the user is presented with a dialog(1) menu to choose which of these should be isntalled. PR: 22818 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
2000-11-13 14:48:49 +01:00
- Update to 5.0.0 PR: ports/122437 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
2008-04-13 09:22:42 +02:00
CONFIGURE_ARGS+= --with-docroot=${DOCSDIR}
- Update EMBOSS (biology/emboss) from 1.9.0 to 1.9.1 - Update the EMBASSY package EMNU from 1.0.2 to 1.0.3 - Merged the four pkg-plist* files into one PR: 24717 Submitted by: MAINTAINER
2001-01-29 16:48:01 +01:00
- Update to 5.0.0 PR: ports/122437 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
2008-04-13 09:22:42 +02:00
.if !defined(WITHOUT_X11)
USE_XORG= x11
Convert from USE_MOTIF to USES=motif While here: - trim headers - Remove indefinite article from comment - convert USE_GMAKE to USES=gmake
2013-07-09 23:49:35 +02:00
USES+= motif
In preparation for making libtool generate libraries with a sane name, fix all LIB_DEPENDS in biology
2013-12-11 15:43:51 +01:00
LIB_DEPENDS+= libgd.so:${PORTSDIR}/graphics/gd \
libpng15.so:${PORTSDIR}/graphics/png
- Update to 5.0.0 PR: ports/122437 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
2008-04-13 09:22:42 +02:00
.else
CONFIGURE_ARGS+= --without-x
- Update to 2.9.0 - Pass maintainership to submitter PR: ports/74333 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar>
2004-11-26 02:11:43 +01:00
.endif
- This is a fairly extensive rework of this port. - "EMBASSY" applications are third party tools which have been adapted to function as part of EMBOSS, but which are not included with the base EMBOSS distribution for licensing or other reasons. This new version of the EMBOSS port now contains the three current EMBASSY applications as well, and during installation the user is presented with a dialog(1) menu to choose which of these should be isntalled. PR: 22818 Submitted by: Johann Visagie <johann@egenetics.com> MAINTAINER
2000-11-13 14:48:49 +01:00
- Update to 5.0.0 PR: ports/122437 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
2008-04-13 09:22:42 +02:00
DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html
CONFIG_FILE= ${WRKSRC}/emboss/emboss.default.template
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 17:55:44 +02:00
NO_STAGE= yes
For EMBOSS: This patch brings EMBOSS up to date with the current version. i. The patches included in files/ are bugfixes for files in EMBOSS-3.0.0 that appeared after the release. They are documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README This is just 'for the record' so that we remember to remove these patches in the next update. ii. EMBOSS is now installed by default in LOCALBASE/emboss This is to avoid CONFLICTS with other ports that install files with the same names. Installing EMBOSS to another PREFIX is also possible. iii. now EMBASSY and EMBOSS both store their distfiles in the same DIST_SUBDIR iv. use built-in PKGMESSAGE and SUB_FILES instead of doing it the old (manual) way For EMBASSY: This update brings embassy in sync with the update of EMBOSS to 3.0.0. Things that changed from previous version of the port: i. embassy now installs by default in $LOCALBASE/emboss (the new default PREFIX for emboss as well). ii. changed DIST_SUBDIR so that all the distfiles are put together with emboss. This makes sense(TM) iii. incorporated new EMBASSY apps (this accounts for the changes in OPTIONS and pkg-plist) iv. removed obsoleted patches Finally, I included a sample text that could go in UPDATING. PR: 93053 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)
2006-03-31 11:43:21 +02:00
pre-install:
@ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${DATADIR}#' ${CONFIG_FILE}
Update to emboss 1.1.0, fixing some style bugs too. PR: ports/20519 Submitted by: Johann Visagie <johann@egenetics.com> (maintainer)
2000-08-12 18:15:48 +02:00
post-install:
For EMBOSS: This patch brings EMBOSS up to date with the current version. i. The patches included in files/ are bugfixes for files in EMBOSS-3.0.0 that appeared after the release. They are documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README This is just 'for the record' so that we remember to remove these patches in the next update. ii. EMBOSS is now installed by default in LOCALBASE/emboss This is to avoid CONFLICTS with other ports that install files with the same names. Installing EMBOSS to another PREFIX is also possible. iii. now EMBASSY and EMBOSS both store their distfiles in the same DIST_SUBDIR iv. use built-in PKGMESSAGE and SUB_FILES instead of doing it the old (manual) way For EMBASSY: This update brings embassy in sync with the update of EMBOSS to 3.0.0. Things that changed from previous version of the port: i. embassy now installs by default in $LOCALBASE/emboss (the new default PREFIX for emboss as well). ii. changed DIST_SUBDIR so that all the distfiles are put together with emboss. This makes sense(TM) iii. incorporated new EMBASSY apps (this accounts for the changes in OPTIONS and pkg-plist) iv. removed obsoleted patches Finally, I included a sample text that could go in UPDATING. PR: 93053 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)
2006-03-31 11:43:21 +02:00
${CHOWN} ${SHAREOWN}:${SHAREGRP} ${DATADIR}/emboss.default.template
Update to emboss 1.1.0, fixing some style bugs too. PR: ports/20519 Submitted by: Johann Visagie <johann@egenetics.com> (maintainer)
2000-08-12 18:15:48 +02:00
@ ${CAT} ${PKGMESSAGE}
Add emboss, the European Molecular Biology Open Software Suite PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com>
2000-07-31 21:13:54 +02:00
.include <bsd.port.mk>
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