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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-08-22 13:59:58 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-08-22 13:59:58 +0000 |
| commit | c5efaea23b875a30e9a7652734d2c992d44f9fbc (patch) | |
| tree | 3643ad563b3cef0bd98483069992fe5cd7b2efcd | |
| parent | 213eef02963155bd76873f679f6e29c7a0abf6ee (diff) | |
| download | ports-c5efaea23b875a30e9a7652734d2c992d44f9fbc.tar.gz ports-c5efaea23b875a30e9a7652734d2c992d44f9fbc.zip | |
biology/bbmap: Update to 38.92
Numerous small fixes and enhancements
Reported by: portscout
| -rw-r--r-- | biology/bbmap/Makefile | 8 | ||||
| -rw-r--r-- | biology/bbmap/distinfo | 6 | ||||
| -rw-r--r-- | biology/bbmap/pkg-plist | 16 |
3 files changed, 22 insertions, 8 deletions
diff --git a/biology/bbmap/Makefile b/biology/bbmap/Makefile index 9f20eab70e8c..9527ee8f4076 100644 --- a/biology/bbmap/Makefile +++ b/biology/bbmap/Makefile @@ -1,5 +1,5 @@ PORTNAME= bbmap -DISTVERSION= 38.90 +DISTVERSION= 38.92 CATEGORIES= biology java MASTER_SITES= SF/bbmap/ DISTNAME= BBMap_${PORTVERSION} @@ -23,7 +23,7 @@ WRKSRC= ${WRKDIR}/${PORTNAME} NO_BUILD= yes NO_ARCH= yes -LIBEXEC_DIR= ${PREFIX}/libexec/bbmap +LIBEXEC_DIR= ${PREFIX}/libexec/bbmap pre-configure: ${REINPLACE_CMD} -e 's|"$$DIR""current/"|${JAVAJARDIR}/bbmap|g' \ @@ -32,13 +32,15 @@ pre-configure: -e 's|"$$DIR""/calcmem.sh"|${LIBEXEC_DIR}/bbmap/calcmem.sh|g' \ ${WRKSRC}/*.sh +# FIXME: Find out which scripts are meant to be part of the CLI do-install: @${MKDIR} ${STAGEDIR}${LIBEXEC_DIR} @${MKDIR} ${STAGEDIR}${JAVAJARDIR}/bbmap ${INSTALL_SCRIPT} ${WRKSRC}/*.sh ${STAGEDIR}${LIBEXEC_DIR} cd ${WRKSRC}/current && ${COPYTREE_SHARE} . \ ${STAGEDIR}${JAVAJARDIR}/bbmap -.for f in bbduk.sh bbnorm.sh dedupe.sh bbmap.sh bloomfilter.sh reformat.sh +.for f in bbduk.sh bbnorm.sh dedupe.sh bbmap.sh bloomfilter.sh reformat.sh \ + bbmerge.sh tadpole.sh ${RLN} ${STAGEDIR}${LIBEXEC_DIR}/${f} ${STAGEDIR}${PREFIX}/bin .endfor diff --git a/biology/bbmap/distinfo b/biology/bbmap/distinfo index 2dcabac6c8b8..391a7c547bee 100644 --- a/biology/bbmap/distinfo +++ b/biology/bbmap/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1618324169 -SHA256 (BBMap_38.90.tar.gz) = a366531c566da5e7246ccf707b6770a92246c1cfe29fd30dc2d800c0d82269f1 -SIZE (BBMap_38.90.tar.gz) = 10516866 +TIMESTAMP = 1629639676 +SHA256 (BBMap_38.92.tar.gz) = a5db3921684296dcbcabd0d36dc123597f587a6ac96855f4f901fee494718dc3 +SIZE (BBMap_38.92.tar.gz) = 10669924 diff --git a/biology/bbmap/pkg-plist b/biology/bbmap/pkg-plist index 195fa6f86ab3..d4d5cbf8b549 100644 --- a/biology/bbmap/pkg-plist +++ b/biology/bbmap/pkg-plist @@ -1,9 +1,11 @@ bin/bbduk.sh bin/bbmap.sh +bin/bbmerge.sh bin/bbnorm.sh bin/bloomfilter.sh bin/dedupe.sh bin/reformat.sh +bin/tadpole.sh libexec/bbmap/a_sample_mt.sh libexec/bbmap/addadapters.sh libexec/bbmap/addssu.sh @@ -1184,6 +1186,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/Seal$ProcessThread.class %%JAVAJARDIR%%/bbmap/jgi/Seal.class %%JAVAJARDIR%%/bbmap/jgi/Seal.java +%%JAVAJARDIR%%/bbmap/jgi/SealRefInfo.class +%%JAVAJARDIR%%/bbmap/jgi/SealRefInfo.java %%JAVAJARDIR%%/bbmap/jgi/Shred.class %%JAVAJARDIR%%/bbmap/jgi/Shred.java %%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$CountComparator.class @@ -1233,8 +1237,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.java %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.class %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.java -%%JAVAJARDIR%%/bbmap/kmer/AtomicShortArray.class -%%JAVAJARDIR%%/bbmap/kmer/AtomicShortArray.java %%JAVAJARDIR%%/bbmap/kmer/DumpThread.class %%JAVAJARDIR%%/bbmap/kmer/DumpThread.java %%JAVAJARDIR%%/bbmap/kmer/HashArray.class @@ -1553,6 +1555,12 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/sort/SortReadsByID$Block.class %%JAVAJARDIR%%/bbmap/sort/SortReadsByID.class %%JAVAJARDIR%%/bbmap/sort/SortReadsByID.java +%%JAVAJARDIR%%/bbmap/star/Ship.class +%%JAVAJARDIR%%/bbmap/star/Ship.java +%%JAVAJARDIR%%/bbmap/star/Simulate.class +%%JAVAJARDIR%%/bbmap/star/Simulate.java +%%JAVAJARDIR%%/bbmap/star/Weapon.class +%%JAVAJARDIR%%/bbmap/star/Weapon.java %%JAVAJARDIR%%/bbmap/stream/ArrayListSet$Pack.class %%JAVAJARDIR%%/bbmap/stream/ArrayListSet.class %%JAVAJARDIR%%/bbmap/stream/ArrayListSet.java @@ -1726,6 +1734,10 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/structures/LongHeapSetInterface.java %%JAVAJARDIR%%/bbmap/structures/LongList.class %%JAVAJARDIR%%/bbmap/structures/LongList.java +%%JAVAJARDIR%%/bbmap/structures/LongList2.class +%%JAVAJARDIR%%/bbmap/structures/LongList2.java +%%JAVAJARDIR%%/bbmap/structures/LongList3.class +%%JAVAJARDIR%%/bbmap/structures/LongList3.java %%JAVAJARDIR%%/bbmap/structures/LongListSet$LongListSetIterator.class %%JAVAJARDIR%%/bbmap/structures/LongListSet.class %%JAVAJARDIR%%/bbmap/structures/LongListSet.java |