From e54e3e4e10f62a2ab36fa76febfca7b657ff8403 Mon Sep 17 00:00:00 2001 From: Johann Visagie Date: Thu, 18 Oct 2001 10:51:57 +0000 Subject: - Updat to version 0.6 - Since Martel is currently only maintained as part of the Biopython distribution, switch to a using locally maintained distfile culled from the Biopython CVS repo, including the "doc" subdirectory from Martel 0.5 --- textproc/py-martel/Makefile | 23 +++---- textproc/py-martel/distinfo | 2 +- textproc/py-martel/pkg-descr | 8 +-- textproc/py-martel/pkg-plist | 159 +++---------------------------------------- 4 files changed, 24 insertions(+), 168 deletions(-) (limited to 'textproc') diff --git a/textproc/py-martel/Makefile b/textproc/py-martel/Makefile index ce089c0ed05d..f5e63657c2e3 100644 --- a/textproc/py-martel/Makefile +++ b/textproc/py-martel/Makefile @@ -6,34 +6,32 @@ # PORTNAME= martel -PORTVERSION= 0.5 -PORTREVISION= 4 +PORTVERSION= 0.6 PORTEPOCH= 1 CATEGORIES= textproc biology python -MASTER_SITES= http://www.biopython.org/~dalke/Martel/ +MASTER_SITES= ${MASTER_SITE_LOCAL} +MASTER_SITE_SUBDIR= wjv PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= Martel-${PORTVERSION} MAINTAINER= wjv@FreeBSD.org +BUILD_DEPENDS= ${PYDISTUTILS} RUN_DEPENDS= ${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base USE_PYTHON= yes - -MARTEL_DIR= ${PREFIX}/lib/${PYTHON_VERSION}/site-packages/Martel -EXAMPLESDIR= ${PREFIX}/share/examples/martel +USE_BZIP2= yes +PYTHON_SETUP= ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py +EXAMPLESDIR= ${PREFIX}/share/examples/${PORTNAME} do-build: - @ ${PYTHON_CMD} ${PYTHON_LIBDIR}/compileall.py ${WRKSRC} - @ ${PYTHON_CMD} -O ${PYTHON_LIBDIR}/compileall.py ${WRKSRC} + @ cd ${WRKSRC} && ${PYTHON_SETUP} build pre-install: @ ${SH} ${PKGREQ} INSTALL do-install: - @ ${MKDIR} ${MARTEL_DIR} - @ (cd ${WRKSRC} && find *.py *.pyc *.pyo formats test \ - | cpio --quiet -pdum -R ${BINOWN}:${BINGRP} ${MARTEL_DIR}) + @ cd ${WRKSRC} && ${PYTHON_SETUP} install -c -O1 --prefix=${PREFIX} post-install: .if !defined(NOPORTDOCS) @@ -41,9 +39,8 @@ post-install: .for docfile in README HISTORY doc/* @ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR} .endfor - @ ${MKDIR} ${EXAMPLESDIR}/builders + @ ${MKDIR} ${EXAMPLESDIR} @ ${INSTALL_DATA} ${WRKSRC}/examples/* ${EXAMPLESDIR} - @ ${INSTALL_DATA} ${WRKSRC}/builders/* ${EXAMPLESDIR}/builders .endif .include diff --git a/textproc/py-martel/distinfo b/textproc/py-martel/distinfo index 01b4d1a11d03..d45bf3171ca0 100644 --- a/textproc/py-martel/distinfo +++ b/textproc/py-martel/distinfo @@ -1 +1 @@ -MD5 (Martel-0.5.tar.gz) = 97f78433f8b6bfbedcf99d7ca1bc887d +MD5 (Martel-0.6.tar.bz2) = f7d720ff6169c75a588ea4e8e2a8542b diff --git a/textproc/py-martel/pkg-descr b/textproc/py-martel/pkg-descr index 6a3e6639643f..4005d54710bc 100644 --- a/textproc/py-martel/pkg-descr +++ b/textproc/py-martel/pkg-descr @@ -10,10 +10,8 @@ Biopython - http://www.biopython.org/) where there is often a need to parse flat and semi-structured legacy file formats. However, it is generally applicable to the parsing of such files in all fields of endeavour. -More information on Martel may be found in this conference poster: -http://www.biopython.org/~dalke/Martel/BOSC2000.poster/ - -Author: Andrew Dalke -WWW: http://www.biopython.org/~dalke/Martel/ +Author: Andrew Dalke +WWW: http://www.dalkescientific.com/Martel/ +See also: http://www.biopython.org/~dalke/Martel/ -- Johann Visagie diff --git a/textproc/py-martel/pkg-plist b/textproc/py-martel/pkg-plist index f4c8d1d84886..79d57c139a63 100644 --- a/textproc/py-martel/pkg-plist +++ b/textproc/py-martel/pkg-plist @@ -3,6 +3,9 @@ %%PORTDOCS%%share/doc/martel/intro.txt %%PORTDOCS%%share/doc/martel/tech_description.txt %%PORTDOCS%%share/doc/martel/writing_a_format.txt +%%PORTDOCS%%share/examples/martel/sample.comma +%%PORTDOCS%%share/examples/martel/sample.swissprot +%%PORTDOCS%%share/examples/martel/sample.tab lib/%%PYTHON_VERSION%%/site-packages/Martel/Expression.py lib/%%PYTHON_VERSION%%/site-packages/Martel/Expression.pyc lib/%%PYTHON_VERSION%%/site-packages/Martel/Expression.pyo @@ -24,157 +27,15 @@ lib/%%PYTHON_VERSION%%/site-packages/Martel/__init__.pyo lib/%%PYTHON_VERSION%%/site-packages/Martel/convert_re.py lib/%%PYTHON_VERSION%%/site-packages/Martel/convert_re.pyc lib/%%PYTHON_VERSION%%/site-packages/Martel/convert_re.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/GenBank.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/GenBank.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/GenBank.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/MDL_10_1996.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/MDL_10_1996.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/MDL_10_1996.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/PDB_2_1.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/PDB_2_1.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/PDB_2_1.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/PIR_3_0.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/PIR_3_0.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/PIR_3_0.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/__init__.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/__init__.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/__init__.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blastall_2_0_10.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blastall_2_0_10.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blastall_2_0_10.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blocks_12.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blocks_12.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blocks_12.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blocksplus.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blocksplus.pyc 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-lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/prosite16.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/swissprot38.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/swissprot38.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/swissprot38.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/taxonomy.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/taxonomy.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/taxonomy.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/trembl14.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/trembl14.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/trembl14.pyo +lib/%%PYTHON_VERSION%%/site-packages/Martel/msre_constants.py +lib/%%PYTHON_VERSION%%/site-packages/Martel/msre_constants.pyc +lib/%%PYTHON_VERSION%%/site-packages/Martel/msre_constants.pyo +lib/%%PYTHON_VERSION%%/site-packages/Martel/msre_parse.py +lib/%%PYTHON_VERSION%%/site-packages/Martel/msre_parse.pyc 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-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Expression.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Expression.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Expression.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_GenBank.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_GenBank.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_GenBank.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Generate.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Generate.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Generate.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Iterator.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Iterator.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Iterator.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_MDL_10_1996.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_MDL_10_1996.pyc 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-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_primers.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_prodoc16.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_prodoc16.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_prodoc16.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_prosite16.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_prosite16.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_prosite16.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_swissprot38.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_swissprot38.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_swissprot38.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_taxonomy.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_taxonomy.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_taxonomy.pyo -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_trembl14.py -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_trembl14.pyc -lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_trembl14.pyo -share/examples/martel/README -share/examples/martel/builders/SwissProtBuilder.py -share/examples/martel/builders/SwissProtBuilder.pyc -share/examples/martel/builders/SwissProtBuilder.pyo -share/examples/martel/pdb1plm.ent -share/examples/martel/sample.swissprot -share/examples/martel/swissprot2html.py -share/examples/martel/swissprot2html.pyc -share/examples/martel/swissprot2html.pyo -share/examples/martel/test.mol -share/examples/martel/toxml.py -share/examples/martel/toxml.pyc -share/examples/martel/toxml.pyo -@dirrm share/examples/martel/builders -@dirrm share/examples/martel -@dirrm lib/%%PYTHON_VERSION%%/site-packages/Martel/test -@dirrm lib/%%PYTHON_VERSION%%/site-packages/Martel/formats @dirrm lib/%%PYTHON_VERSION%%/site-packages/Martel +%%PORTDOCS%%@dirrm share/examples/martel %%PORTDOCS%%@dirrm share/doc/martel -- cgit v1.2.3