diff options
| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-04-19 16:40:52 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-04-19 16:41:58 +0000 |
| commit | 3bc87a0f1a1b36d958c9478a0d2feaeebf283dbe (patch) | |
| tree | 22afd10872067fc11fc408a2f0d0d29302a0265b /biology | |
| parent | fdcd56b5176c83a08c4f273ce2f78ab2f29c2a79 (diff) | |
| download | ports-3bc87a0f1a1b36d958c9478a0d2feaeebf283dbe.tar.gz ports-3bc87a0f1a1b36d958c9478a0d2feaeebf283dbe.zip | |
biology/snpeff: Improvements to Makefile and patches
Reported by: Omp
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/snpeff/Makefile | 11 | ||||
| -rw-r--r-- | biology/snpeff/distinfo | 6 | ||||
| -rw-r--r-- | biology/snpeff/files/patch-scripts_snpEff | 4 | ||||
| -rw-r--r-- | biology/snpeff/files/patch-scripts_snpSift | 4 |
4 files changed, 13 insertions, 12 deletions
diff --git a/biology/snpeff/Makefile b/biology/snpeff/Makefile index 3973e9a9a792..81cf1d4f56e1 100644 --- a/biology/snpeff/Makefile +++ b/biology/snpeff/Makefile @@ -3,6 +3,7 @@ DISTVERSION= 5.0 CATEGORIES= biology java python MASTER_SITES= https://snpeff.blob.core.windows.net/versions/ DISTNAME= snpEff_latest_core +DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Genetic variant annotation and effect prediction toolbox @@ -24,6 +25,11 @@ WRKSRC= ${WRKDIR}/snpEff LIBEXEC_DIR= ${PREFIX}/libexec/snpeff +pre-configure: + ${REINPLACE_CMD} -e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g' \ + -e 's|%%JAVA_HOME%%|${JAVA_HOME}|g' \ + ${WRKSRC}/scripts/snpEff ${WRKSRC}/scripts/snpSift + do-install: ${MKDIR} ${STAGEDIR}${JAVAJARDIR}/snpeff ${MKDIR} ${STAGEDIR}${LIBEXEC_DIR} @@ -33,9 +39,4 @@ do-install: ${INSTALL_DATA} ${WRKSRC}/*.config ${STAGEDIR}${JAVAJARDIR}/snpeff cd ${WRKSRC}/scripts && ${COPYTREE_BIN} . ${STAGEDIR}${LIBEXEC_DIR} -pre-configure: - ${REINPLACE_CMD} -e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g' \ - -e 's|%%PREFIX%%|${PREFIX}|g' \ - ${WRKSRC}/scripts/snpEff ${WRKSRC}/scripts/snpSift - .include <bsd.port.mk> diff --git a/biology/snpeff/distinfo b/biology/snpeff/distinfo index 895315e4a8c3..decfc79a708d 100644 --- a/biology/snpeff/distinfo +++ b/biology/snpeff/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1618353537 -SHA256 (snpEff_latest_core.zip) = 85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d -SIZE (snpEff_latest_core.zip) = 45828841 +TIMESTAMP = 1618847647 +SHA256 (snpeff-5.0/snpEff_latest_core.zip) = 85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d +SIZE (snpeff-5.0/snpEff_latest_core.zip) = 45828841 diff --git a/biology/snpeff/files/patch-scripts_snpEff b/biology/snpeff/files/patch-scripts_snpEff index dace484960d7..d15b83ad84e0 100644 --- a/biology/snpeff/files/patch-scripts_snpEff +++ b/biology/snpeff/files/patch-scripts_snpEff @@ -1,4 +1,4 @@ ---- scripts/snpEff.orig 2021-04-13 22:55:13 UTC +--- scripts/snpEff.orig 2021-04-19 15:55:06 UTC +++ scripts/snpEff @@ -13,9 +13,10 @@ # Created by: Brad Chapman @@ -7,7 +7,7 @@ -jardir="$(cd "$(dirname "$0")" && cd ".." && pwd -P)" +jardir=%%JAVAJARDIR%%/snpeff +userdir=~/snpEff -+JAVA_HOME=%%PREFIX%%/openjdk12 ++JAVA_HOME=%%JAVA_HOME%% -java=java if [ -e "$JAVA_HOME/bin/java" ] diff --git a/biology/snpeff/files/patch-scripts_snpSift b/biology/snpeff/files/patch-scripts_snpSift index 838875a344f8..c76fa3c4fcfd 100644 --- a/biology/snpeff/files/patch-scripts_snpSift +++ b/biology/snpeff/files/patch-scripts_snpSift @@ -1,4 +1,4 @@ ---- scripts/snpSift.orig 2021-04-13 22:40:00 UTC +--- scripts/snpSift.orig 2021-04-19 15:55:06 UTC +++ scripts/snpSift @@ -13,9 +13,9 @@ # Created by: Brad Chapman @@ -6,7 +6,7 @@ -jardir="$(cd "$(dirname "$0")" && cd ".." && pwd -P)" +jardir=%%JAVAJARDIR%%/snpeff -+JAVA_HOME=%%PREFIX%%/openjdk12 ++JAVA_HOME=%%JAVA_HOME%% -java=java if [ -e "$JAVA_HOME/bin/java" ] |