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biology/bbmap: Update to 38.92

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Numerous small fixes and enhancements

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2021-08-22 08:59:58 -05:00
parent 213eef0296
commit c5efaea23b
3 changed files with 22 additions and 8 deletions
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8
biology/bbmap/Makefile
View file

@ -1,5 +1,5 @@
PORTNAME= bbmap PORTNAME= bbmap
DISTVERSION= 38.90 DISTVERSION= 38.92
CATEGORIES= biology java CATEGORIES= biology java
MASTER_SITES= SF/bbmap/ MASTER_SITES= SF/bbmap/
DISTNAME= BBMap_${PORTVERSION} DISTNAME= BBMap_${PORTVERSION}
@ -23,7 +23,7 @@ WRKSRC= ${WRKDIR}/${PORTNAME}
NO_BUILD= yes NO_BUILD= yes
NO_ARCH= yes NO_ARCH= yes
LIBEXEC_DIR= ${PREFIX}/libexec/bbmap LIBEXEC_DIR= ${PREFIX}/libexec/bbmap
pre-configure: pre-configure:
${REINPLACE_CMD} -e 's|"$$DIR""current/"|${JAVAJARDIR}/bbmap|g' \ ${REINPLACE_CMD} -e 's|"$$DIR""current/"|${JAVAJARDIR}/bbmap|g' \
@ -32,13 +32,15 @@ pre-configure:
-e 's|"$$DIR""/calcmem.sh"|${LIBEXEC_DIR}/bbmap/calcmem.sh|g' \ -e 's|"$$DIR""/calcmem.sh"|${LIBEXEC_DIR}/bbmap/calcmem.sh|g' \
${WRKSRC}/*.sh ${WRKSRC}/*.sh
# FIXME: Find out which scripts are meant to be part of the CLI
do-install: do-install:
@${MKDIR} ${STAGEDIR}${LIBEXEC_DIR} @${MKDIR} ${STAGEDIR}${LIBEXEC_DIR}
@${MKDIR} ${STAGEDIR}${JAVAJARDIR}/bbmap @${MKDIR} ${STAGEDIR}${JAVAJARDIR}/bbmap
${INSTALL_SCRIPT} ${WRKSRC}/*.sh ${STAGEDIR}${LIBEXEC_DIR} ${INSTALL_SCRIPT} ${WRKSRC}/*.sh ${STAGEDIR}${LIBEXEC_DIR}
cd ${WRKSRC}/current && ${COPYTREE_SHARE} . \ cd ${WRKSRC}/current && ${COPYTREE_SHARE} . \
${STAGEDIR}${JAVAJARDIR}/bbmap ${STAGEDIR}${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 ${RLN} ${STAGEDIR}${LIBEXEC_DIR}/${f} ${STAGEDIR}${PREFIX}/bin
.endfor .endfor

6
biology/bbmap/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1618324169 TIMESTAMP = 1629639676
SHA256 (BBMap_38.90.tar.gz) = a366531c566da5e7246ccf707b6770a92246c1cfe29fd30dc2d800c0d82269f1 SHA256 (BBMap_38.92.tar.gz) = a5db3921684296dcbcabd0d36dc123597f587a6ac96855f4f901fee494718dc3
SIZE (BBMap_38.90.tar.gz) = 10516866 SIZE (BBMap_38.92.tar.gz) = 10669924

16
biology/bbmap/pkg-plist
View file

@ -1,9 +1,11 @@
bin/bbduk.sh bin/bbduk.sh
bin/bbmap.sh bin/bbmap.sh
bin/bbmerge.sh
bin/bbnorm.sh bin/bbnorm.sh
bin/bloomfilter.sh bin/bloomfilter.sh
bin/dedupe.sh bin/dedupe.sh
bin/reformat.sh bin/reformat.sh
bin/tadpole.sh
libexec/bbmap/a_sample_mt.sh libexec/bbmap/a_sample_mt.sh
libexec/bbmap/addadapters.sh libexec/bbmap/addadapters.sh
libexec/bbmap/addssu.sh libexec/bbmap/addssu.sh
@ -1184,6 +1186,8 @@ libexec/bbmap/webcheck.sh
%%JAVAJARDIR%%/bbmap/jgi/Seal$ProcessThread.class %%JAVAJARDIR%%/bbmap/jgi/Seal$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/Seal.class %%JAVAJARDIR%%/bbmap/jgi/Seal.class
%%JAVAJARDIR%%/bbmap/jgi/Seal.java %%JAVAJARDIR%%/bbmap/jgi/Seal.java
%%JAVAJARDIR%%/bbmap/jgi/SealRefInfo.class
%%JAVAJARDIR%%/bbmap/jgi/SealRefInfo.java
%%JAVAJARDIR%%/bbmap/jgi/Shred.class %%JAVAJARDIR%%/bbmap/jgi/Shred.class
%%JAVAJARDIR%%/bbmap/jgi/Shred.java %%JAVAJARDIR%%/bbmap/jgi/Shred.java
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$CountComparator.class %%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$CountComparator.class
@ -1233,8 +1237,6 @@ libexec/bbmap/webcheck.sh
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.java %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.java
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.class %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.class
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.java %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.java
%%JAVAJARDIR%%/bbmap/kmer/AtomicShortArray.class
%%JAVAJARDIR%%/bbmap/kmer/AtomicShortArray.java
%%JAVAJARDIR%%/bbmap/kmer/DumpThread.class %%JAVAJARDIR%%/bbmap/kmer/DumpThread.class
%%JAVAJARDIR%%/bbmap/kmer/DumpThread.java %%JAVAJARDIR%%/bbmap/kmer/DumpThread.java
%%JAVAJARDIR%%/bbmap/kmer/HashArray.class %%JAVAJARDIR%%/bbmap/kmer/HashArray.class
@ -1553,6 +1555,12 @@ libexec/bbmap/webcheck.sh
%%JAVAJARDIR%%/bbmap/sort/SortReadsByID$Block.class %%JAVAJARDIR%%/bbmap/sort/SortReadsByID$Block.class
%%JAVAJARDIR%%/bbmap/sort/SortReadsByID.class %%JAVAJARDIR%%/bbmap/sort/SortReadsByID.class
%%JAVAJARDIR%%/bbmap/sort/SortReadsByID.java %%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$Pack.class %%JAVAJARDIR%%/bbmap/stream/ArrayListSet$Pack.class
%%JAVAJARDIR%%/bbmap/stream/ArrayListSet.class %%JAVAJARDIR%%/bbmap/stream/ArrayListSet.class
%%JAVAJARDIR%%/bbmap/stream/ArrayListSet.java %%JAVAJARDIR%%/bbmap/stream/ArrayListSet.java
@ -1726,6 +1734,10 @@ libexec/bbmap/webcheck.sh
%%JAVAJARDIR%%/bbmap/structures/LongHeapSetInterface.java %%JAVAJARDIR%%/bbmap/structures/LongHeapSetInterface.java
%%JAVAJARDIR%%/bbmap/structures/LongList.class %%JAVAJARDIR%%/bbmap/structures/LongList.class
%%JAVAJARDIR%%/bbmap/structures/LongList.java %%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$LongListSetIterator.class %%JAVAJARDIR%%/bbmap/structures/LongListSet$LongListSetIterator.class
%%JAVAJARDIR%%/bbmap/structures/LongListSet.class %%JAVAJARDIR%%/bbmap/structures/LongListSet.class
%%JAVAJARDIR%%/bbmap/structures/LongListSet.java %%JAVAJARDIR%%/bbmap/structures/LongListSet.java