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pkgsrc/biology/lucy/Makefile

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Remove pkgviews: don't set PKG_INSTALLATION_TYPES in Makefiles.
2014-10-09 16:05:50 +02:00
# $NetBSD: Makefile,v 1.9 2014/10/09 14:06:01 wiz Exp $
Import lucy from pkgsrc-wip. Packaged by David Price and modified by me. A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly,possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal. The primary advantage of Lucy over other similar utilities is that it is a fully integrated, stand alone program.
2005-03-26 18:05:01 +01:00
#
Update lucy to 1.20. Based on PR#43777 by Kamel Derouiche, with some clean up by me. Version 1.20, 9/3/2008. This version fixes a bug that caused lucy to fail when there was too much information on the FASTA header lines in the input files. Lucy had a 256 character buffer for reading lines from the input files. If any FASTA header lines were longer than 256 characters, the remaining characters would get read as part of the FASTA sequence. The solution implemented in this version is simply to increase the buffer size to 4096 characters. While that still leaves the potential for the same error to occur with extremely long header lines, the limitation that this entails seems reasonable, and this should fix the problem for all pratical purposes. --------------------------------------------------------------------- Version 1.19, 12/30/2003. This version fixes a bug that could cause sequences to be rejected incorrectly in the vector detection step (phase 6). Because of the way that lucy compares "tags" in the target sequence with "tags" in the vector sequence, some bases in the target sequence could get counted more than once in the tally of bases that match the vector sequence. In rare instances, this could cause the sequence to exceed the minimum threshold for rejection, as a result of random sequence similarity. The reporting of the CLB range in the -debug output file has also been changed. If the CLB range begins with the first base of the sequence, then the left coordinate of the CLB range will be reported as 1 (instead of 0). The range "CLB 0 0" still indicates an empty CLB range.
2010-09-19 09:13:37 +02:00
DISTNAME= ${PKGNAME:S/-//}
PKGNAME= lucy-1.20
Import lucy from pkgsrc-wip. Packaged by David Price and modified by me. A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly,possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal. The primary advantage of Lucy over other similar utilities is that it is a fully integrated, stand alone program.
2005-03-26 18:05:01 +01:00
CATEGORIES= biology
Update lucy to 1.20. Based on PR#43777 by Kamel Derouiche, with some clean up by me. Version 1.20, 9/3/2008. This version fixes a bug that caused lucy to fail when there was too much information on the FASTA header lines in the input files. Lucy had a 256 character buffer for reading lines from the input files. If any FASTA header lines were longer than 256 characters, the remaining characters would get read as part of the FASTA sequence. The solution implemented in this version is simply to increase the buffer size to 4096 characters. While that still leaves the potential for the same error to occur with extremely long header lines, the limitation that this entails seems reasonable, and this should fix the problem for all pratical purposes. --------------------------------------------------------------------- Version 1.19, 12/30/2003. This version fixes a bug that could cause sequences to be rejected incorrectly in the vector detection step (phase 6). Because of the way that lucy compares "tags" in the target sequence with "tags" in the vector sequence, some bases in the target sequence could get counted more than once in the tally of bases that match the vector sequence. In rare instances, this could cause the sequence to exceed the minimum threshold for rejection, as a result of random sequence similarity. The reporting of the CLB range in the -debug output file has also been changed. If the CLB range begins with the first base of the sequence, then the left coordinate of the CLB range will be reported as 1 (instead of 0). The range "CLB 0 0" still indicates an empty CLB range.
2010-09-19 09:13:37 +02:00
MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=lucy/}
Import lucy from pkgsrc-wip. Packaged by David Price and modified by me. A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly,possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal. The primary advantage of Lucy over other similar utilities is that it is a fully integrated, stand alone program.
2005-03-26 18:05:01 +01:00
MAINTAINER= dprice@cs.nmsu.edu
update homepage, update master site.
2009-05-17 01:40:13 +02:00
HOMEPAGE= http://lucy.sourceforge.net/
Import lucy from pkgsrc-wip. Packaged by David Price and modified by me. A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly,possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal. The primary advantage of Lucy over other similar utilities is that it is a fully integrated, stand alone program.
2005-03-26 18:05:01 +01:00
COMMENT= Sequence Cleanup Program
Update lucy to 1.20. Based on PR#43777 by Kamel Derouiche, with some clean up by me. Version 1.20, 9/3/2008. This version fixes a bug that caused lucy to fail when there was too much information on the FASTA header lines in the input files. Lucy had a 256 character buffer for reading lines from the input files. If any FASTA header lines were longer than 256 characters, the remaining characters would get read as part of the FASTA sequence. The solution implemented in this version is simply to increase the buffer size to 4096 characters. While that still leaves the potential for the same error to occur with extremely long header lines, the limitation that this entails seems reasonable, and this should fix the problem for all pratical purposes. --------------------------------------------------------------------- Version 1.19, 12/30/2003. This version fixes a bug that could cause sequences to be rejected incorrectly in the vector detection step (phase 6). Because of the way that lucy compares "tags" in the target sequence with "tags" in the vector sequence, some bases in the target sequence could get counted more than once in the tally of bases that match the vector sequence. In rare instances, this could cause the sequence to exceed the minimum threshold for rejection, as a result of random sequence similarity. The reporting of the CLB range in the -debug output file has also been changed. If the CLB range begins with the first base of the sequence, then the left coordinate of the CLB range will be reported as 1 (instead of 0). The range "CLB 0 0" still indicates an empty CLB range.
2010-09-19 09:13:37 +02:00
#LICENSE= LICENSE file say "artistic", but bit differ.
Import lucy from pkgsrc-wip. Packaged by David Price and modified by me. A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly,possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal. The primary advantage of Lucy over other similar utilities is that it is a fully integrated, stand alone program.
2005-03-26 18:05:01 +01:00
Update lucy to 1.20. Based on PR#43777 by Kamel Derouiche, with some clean up by me. Version 1.20, 9/3/2008. This version fixes a bug that caused lucy to fail when there was too much information on the FASTA header lines in the input files. Lucy had a 256 character buffer for reading lines from the input files. If any FASTA header lines were longer than 256 characters, the remaining characters would get read as part of the FASTA sequence. The solution implemented in this version is simply to increase the buffer size to 4096 characters. While that still leaves the potential for the same error to occur with extremely long header lines, the limitation that this entails seems reasonable, and this should fix the problem for all pratical purposes. --------------------------------------------------------------------- Version 1.19, 12/30/2003. This version fixes a bug that could cause sequences to be rejected incorrectly in the vector detection step (phase 6). Because of the way that lucy compares "tags" in the target sequence with "tags" in the vector sequence, some bases in the target sequence could get counted more than once in the tally of bases that match the vector sequence. In rare instances, this could cause the sequence to exceed the minimum threshold for rejection, as a result of random sequence similarity. The reporting of the CLB range in the -debug output file has also been changed. If the CLB range begins with the first base of the sequence, then the left coordinate of the CLB range will be reported as 1 (instead of 0). The range "CLB 0 0" still indicates an empty CLB range.
2010-09-19 09:13:37 +02:00
WRKSRC= ${WRKDIR}/${PKGNAME_NOREV}p
Made the Makefile simpler. Removed unnecessary .gz suffix from man pages.
2009-06-12 21:07:29 +02:00
AUTO_MKDIRS= yes
Update lucy to 1.20. Based on PR#43777 by Kamel Derouiche, with some clean up by me. Version 1.20, 9/3/2008. This version fixes a bug that caused lucy to fail when there was too much information on the FASTA header lines in the input files. Lucy had a 256 character buffer for reading lines from the input files. If any FASTA header lines were longer than 256 characters, the remaining characters would get read as part of the FASTA sequence. The solution implemented in this version is simply to increase the buffer size to 4096 characters. While that still leaves the potential for the same error to occur with extremely long header lines, the limitation that this entails seems reasonable, and this should fix the problem for all pratical purposes. --------------------------------------------------------------------- Version 1.19, 12/30/2003. This version fixes a bug that could cause sequences to be rejected incorrectly in the vector detection step (phase 6). Because of the way that lucy compares "tags" in the target sequence with "tags" in the vector sequence, some bases in the target sequence could get counted more than once in the tally of bases that match the vector sequence. In rare instances, this could cause the sequence to exceed the minimum threshold for rejection, as a result of random sequence similarity. The reporting of the CLB range in the -debug output file has also been changed. If the CLB range begins with the first base of the sequence, then the left coordinate of the CLB range will be reported as 1 (instead of 0). The range "CLB 0 0" still indicates an empty CLB range.
2010-09-19 09:13:37 +02:00
PTHREAD_AUTO_VARS= yes
Import lucy from pkgsrc-wip. Packaged by David Price and modified by me. A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly,possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal. The primary advantage of Lucy over other similar utilities is that it is a fully integrated, stand alone program.
2005-03-26 18:05:01 +01:00
do-install:
Mechanical changes to add full DESTDIR support to packages that install their files via a custom do-install target.
2008-03-03 01:51:43 +01:00
${INSTALL_PROGRAM} ${WRKSRC}/lucy ${DESTDIR}${PREFIX}/bin
Update lucy to 1.20. Based on PR#43777 by Kamel Derouiche, with some clean up by me. Version 1.20, 9/3/2008. This version fixes a bug that caused lucy to fail when there was too much information on the FASTA header lines in the input files. Lucy had a 256 character buffer for reading lines from the input files. If any FASTA header lines were longer than 256 characters, the remaining characters would get read as part of the FASTA sequence. The solution implemented in this version is simply to increase the buffer size to 4096 characters. While that still leaves the potential for the same error to occur with extremely long header lines, the limitation that this entails seems reasonable, and this should fix the problem for all pratical purposes. --------------------------------------------------------------------- Version 1.19, 12/30/2003. This version fixes a bug that could cause sequences to be rejected incorrectly in the vector detection step (phase 6). Because of the way that lucy compares "tags" in the target sequence with "tags" in the vector sequence, some bases in the target sequence could get counted more than once in the tally of bases that match the vector sequence. In rare instances, this could cause the sequence to exceed the minimum threshold for rejection, as a result of random sequence similarity. The reporting of the CLB range in the -debug output file has also been changed. If the CLB range begins with the first base of the sequence, then the left coordinate of the CLB range will be reported as 1 (instead of 0). The range "CLB 0 0" still indicates an empty CLB range.
2010-09-19 09:13:37 +02:00
${INSTALL_MAN} ${WRKSRC}/lucy.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
Made the Makefile simpler. Removed unnecessary .gz suffix from man pages.
2009-06-12 21:07:29 +02:00
cd ${WRKSRC} && ${INSTALL_DATA} PUC19 PUC19splice PUC19splice.for \
PUC19splice.rev atie.seq atie.qul atie.2nd pSPORT1splice \
pSPORT1vector ARMTM40TR.seq ARMTM40TR.qul lucy.ps lucy.debug \
Mechanical changes to add full DESTDIR support to packages that install their files via a custom do-install target.
2008-03-03 01:51:43 +01:00
${DESTDIR}${PREFIX}/share/examples/lucy
Import lucy from pkgsrc-wip. Packaged by David Price and modified by me. A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly,possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal. The primary advantage of Lucy over other similar utilities is that it is a fully integrated, stand alone program.
2005-03-26 18:05:01 +01:00
.include "../../mk/pthread.buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
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