Date: Sat, 13 Jun 2020 13:54:47 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r538672 - in head/biology: . picard-tools picard-tools/files Message-ID: <202006131354.05DDslB6089429@repo.freebsd.org>
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Author: jwb Date: Sat Jun 13 13:54:47 2020 New Revision: 538672 URL: https://svnweb.freebsd.org/changeset/ports/538672 Log: biology/picard-tools: CLI tools for manipulating sequencing data Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. Added: head/biology/picard-tools/ head/biology/picard-tools/Makefile (contents, props changed) head/biology/picard-tools/buildlog-12-1-amd64-wip-picard-tools (contents, props changed) head/biology/picard-tools/distinfo (contents, props changed) head/biology/picard-tools/files/ head/biology/picard-tools/files/picard.in (contents, props changed) head/biology/picard-tools/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sat Jun 13 13:42:12 2020 (r538671) +++ head/biology/Makefile Sat Jun 13 13:54:47 2020 (r538672) @@ -114,6 +114,7 @@ SUBDIR += phred SUBDIR += phylip SUBDIR += phyml + SUBDIR += picard-tools SUBDIR += plink SUBDIR += primer3 SUBDIR += prodigal Added: head/biology/picard-tools/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/picard-tools/Makefile Sat Jun 13 13:54:47 2020 (r538672) @@ -0,0 +1,35 @@ +# $FreeBSD$ + +PORTNAME= picard +DISTVERSION= 2.22.9 +CATEGORIES= biology java +MASTER_SITES= http://github.com/broadinstitute/picard/releases/download/${PORTVERSION}/ +PKGNAMESUFFIX= -tools +DISTNAME= ${PORTNAME} +EXTRACT_SUFX= .jar + +MAINTAINER= jwb@FreeBSD.org +COMMENT= CLI tools for manipulating high-throughput sequencing (HTS) data + +LICENSE= MIT + +RUN_DEPENDS= samtools:biology/samtools + +USE_JAVA= 1.8+ +JAVA_RUN= yes + +SUB_FILES= picard +NO_BUILD= yes +NO_ARCH= yes + +PLIST_FILES= bin/picard ${JAVAJARDIR}/picard.jar + +do-extract: + # No extract + +do-install: + ${INSTALL_DATA} ${DISTDIR}/${DISTNAME}${EXTRACT_SUFX} \ + ${STAGEDIR}${JAVAJARDIR} + ${INSTALL_SCRIPT} ${WRKDIR}/picard ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> Added: head/biology/picard-tools/buildlog-12-1-amd64-wip-picard-tools ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/picard-tools/buildlog-12-1-amd64-wip-picard-tools Sat Jun 13 13:54:47 2020 (r538672) @@ -0,0 +1,112 @@ +[00:00:00] Creating the reference jail... done +[00:00:07] Mounting system devices for 12-1-amd64-default +[00:00:07] Mounting ports/packages/distfiles +[00:00:07] Stashing existing package repository +[00:00:07] Mounting packages from: /usr/local/poudriere/data/packages/12-1-amd64-default +/etc/resolv.conf -> /usr/local/poudriere/data/.m/12-1-amd64-default/ref/etc/resolv.conf +[00:00:07] Starting jail 12-1-amd64-default +[00:00:07] Ports supports: FLAVORS SELECTED_OPTIONS +[00:00:07] Logs: /usr/local/poudriere/data/logs/bulk/12-1-amd64-default/2020-06-06_19h05m44s +[00:00:07] Loading MOVED for /usr/local/poudriere/data/.m/12-1-amd64-default/ref/usr/ports +[00:00:08] Gathering ports metadata +[00:00:10] Calculating ports order and dependencies +[00:00:11] Sanity checking the repository +[00:00:11] Checking packages for incremental rebuild needs +[00:00:11] Deleting bison-3.5.3,1.txz: new version: 3.5.4,1 +[00:00:11] Deleting fontconfig-2.13.1_1,1.txz: new version: 2.13.92_1,1 +[00:00:11] Deleting libX11-1.6.9,1.txz: new version: 1.6.9_1,1 +[00:00:11] Deleting libedit-3.1.20191211,1.txz: new version: 3.1.20191231,1 +[00:00:11] Deleting libtasn1-4.15.0.txz: new version: 4.16.0 +[00:00:11] Deleting libunwind-20170615.txz: new version: 20170615_1 +[00:00:11] Deleting p11-kit-0.23.18.1.txz: new version: 0.23.20 +[00:00:11] Deleting swig30-3.0.12.txz: new version: 3.0.12_1 +[00:00:11] Deleting xorgproto-2019.2.txz: new version: 2020.1 +[00:00:11] Deleting cairo-1.16.0,2.txz: missing dependency: fontconfig-2.13.1_1,1 +[00:00:11] Deleting dbus-1.12.16.txz: missing dependency: libX11-1.6.9,1 +[00:00:11] Deleting dejavu-2.37_1.txz: missing dependency: fontconfig-2.13.1_1,1 +[00:00:11] Deleting gnutls-3.6.13.txz: missing dependency: ca_root_nss-3.51 +[00:00:11] Deleting libXdamage-1.1.5.txz: missing dependency: libX11-1.6.9,1 +[00:00:11] Deleting libXdmcp-1.1.3.txz: missing dependency: xorgproto-2019.2 +[00:00:11] Deleting libXext-1.3.4,1.txz: missing dependency: libX11-1.6.9,1 +[00:00:11] Deleting libXfixes-5.0.3_2.txz: missing dependency: libX11-1.6.9,1 +[00:00:11] Deleting libXrender-0.9.10_2.txz: missing dependency: libX11-1.6.9,1 +[00:00:11] Deleting libXt-1.2.0,1.txz: missing dependency: libX11-1.6.9,1 +[00:00:11] Deleting libXxf86vm-1.1.4_3.txz: missing dependency: libX11-1.6.9,1 +[00:00:11] Deleting libxcb-1.13.1.txz: missing dependency: libXdmcp-1.1.3 +[00:00:11] Deleting llvm80-8.0.1_3.txz: missing dependency: libedit-3.1.20191211,1 +[00:00:11] Deleting lua52-5.2.4.txz: missing dependency: libedit-3.1.20191211,1 +[00:00:11] Deleting mesa-libs-18.3.2_4.txz: missing dependency: libX11-1.6.9,1 +[00:00:11] Deleting avahi-app-0.7_3.txz: missing dependency: dbus-1.12.16 +[00:00:11] Deleting cups-2.2.13.txz: missing dependency: avahi-app-0.7_3 +[00:00:11] Deleting dbus-glib-0.110.txz: missing dependency: dbus-1.12.16 +[00:00:12] Deleting stale symlinks... done +[00:00:12] Deleting empty directories... done +[00:00:12] Cleaning the build queue +[00:00:12] Sanity checking build queue +[00:00:12] Processing PRIORITY_BOOST +[00:00:12] Balancing pool +[00:00:12] Recording filesystem state for prepkg... done +[00:00:12] Building 28 packages using 4 builders +[00:00:12] Starting/Cloning builders +[00:00:39] Hit CTRL+t at any time to see build progress and stats +[00:00:39] [01] [00:00:00] Building x11/xorgproto | xorgproto-2020.1 +[00:00:39] [02] [00:00:00] Building devel/bison | bison-3.5.4,1 +[00:00:39] [03] [00:00:00] Building x11-fonts/fontconfig | fontconfig-2.13.92_1,1 +[00:00:39] [04] [00:00:00] Building security/libtasn1 | libtasn1-4.16.0 +[00:00:52] [01] [00:00:13] Finished x11/xorgproto | xorgproto-2020.1: Success +[00:00:52] [01] [00:00:00] Building x11/libXdmcp | libXdmcp-1.1.3 +[00:01:03] [01] [00:00:11] Finished x11/libXdmcp | libXdmcp-1.1.3: Success +[00:01:04] [01] [00:00:00] Building x11/libxcb | libxcb-1.13.1 +[00:01:07] [04] [00:00:28] Finished security/libtasn1 | libtasn1-4.16.0: Success +[00:01:07] [04] [00:00:00] Building security/p11-kit | p11-kit-0.23.20 +[00:01:27] [03] [00:00:48] Finished x11-fonts/fontconfig | fontconfig-2.13.92_1,1: Success +[00:01:27] [03] [00:00:00] Building java/javavmwrapper | javavmwrapper-2.7.5 +[00:01:30] [03] [00:00:03] Finished java/javavmwrapper | javavmwrapper-2.7.5: Success +[00:01:30] [03] [00:00:00] Building java/bootstrap-openjdk8 | bootstrap-openjdk8-r450802 +[00:01:54] [02] [00:01:15] Finished devel/bison | bison-3.5.4,1: Success +[00:01:54] [02] [00:00:00] Building x11-fonts/dejavu | dejavu-2.37_1 +[00:02:02] [04] [00:00:55] Finished security/p11-kit | p11-kit-0.23.20: Success +[00:02:02] [04] [00:00:00] Building security/gnutls | gnutls-3.6.13 +[00:02:12] [02] [00:00:18] Finished x11-fonts/dejavu | dejavu-2.37_1: Success +[00:02:12] [02] [00:00:00] Building java/java-zoneinfo | java-zoneinfo-2019.b +[00:02:12] [01] [00:01:08] Finished x11/libxcb | libxcb-1.13.1: Success +[00:02:12] [01] [00:00:00] Building x11/libX11 | libX11-1.6.9_1,1 +[00:02:15] [02] [00:00:03] Finished java/java-zoneinfo | java-zoneinfo-2019.b: Success +[00:02:15] [02] [00:00:00] Building devel/libinotify | libinotify-20180201_1 +[00:02:41] [02] [00:00:26] Finished devel/libinotify | libinotify-20180201_1: Success +[00:02:41] [02] [00:00:00] Building shells/bash | bash-5.0.16 +[00:03:46] [03] [00:02:16] Finished java/bootstrap-openjdk8 | bootstrap-openjdk8-r450802: Success +[00:03:46] [03] [00:00:00] Building audio/alsa-lib | alsa-lib-1.1.2_2 +[00:04:41] [02] [00:02:00] Finished shells/bash | bash-5.0.16: Success +[00:04:41] [02] [00:00:00] Building biology/samtools | samtools-1.9 +[00:04:42] [03] [00:00:56] Finished audio/alsa-lib | alsa-lib-1.1.2_2: Success +[00:05:05] [01] [00:02:53] Finished x11/libX11 | libX11-1.6.9_1,1: Success +[00:05:05] [01] [00:00:00] Building x11/libXext | libXext-1.3.4,1 +[00:05:05] [03] [00:00:00] Building x11/libXfixes | libXfixes-5.0.3_2 +[00:05:17] [03] [00:00:12] Finished x11/libXfixes | libXfixes-5.0.3_2: Success +[00:05:17] [03] [00:00:00] Building x11/libXrender | libXrender-0.9.10_2 +[00:05:23] [01] [00:00:18] Finished x11/libXext | libXext-1.3.4,1: Success +[00:05:23] [01] [00:00:00] Building devel/dbus | dbus-1.12.16 +[00:05:32] [02] [00:00:51] Finished biology/samtools | samtools-1.9: Success +[00:05:32] [02] [00:00:00] Building x11/libXi | libXi-1.7.10,1 +[00:05:32] [03] [00:00:15] Finished x11/libXrender | libXrender-0.9.10_2: Success +[00:05:32] [03] [00:00:00] Building x11-toolkits/libXt | libXt-1.2.0,1 +[00:06:01] [02] [00:00:29] Finished x11/libXi | libXi-1.7.10,1: Success +[00:06:01] [02] [00:00:00] Building x11/libXtst | libXtst-1.2.3_2 +[00:06:14] [02] [00:00:13] Finished x11/libXtst | libXtst-1.2.3_2: Success +[00:06:21] [04] [00:04:19] Finished security/gnutls | gnutls-3.6.13: Success +[00:06:23] [03] [00:00:51] Finished x11-toolkits/libXt | libXt-1.2.0,1: Success +[00:06:35] [01] [00:01:12] Finished devel/dbus | dbus-1.12.16: Success +[00:06:35] [01] [00:00:00] Building devel/dbus-glib | dbus-glib-0.110 +[00:07:01] [01] [00:00:26] Finished devel/dbus-glib | dbus-glib-0.110: Success +[00:07:02] [01] [00:00:00] Building net/avahi-app | avahi-app-0.7_3 +[00:07:56] [01] [00:00:54] Finished net/avahi-app | avahi-app-0.7_3: Success +[00:07:56] [01] [00:00:00] Building print/cups | cups-2.2.13 +[00:09:09] [01] [00:01:13] Finished print/cups | cups-2.2.13: Success +[00:09:09] [01] [00:00:00] Building java/openjdk8 | openjdk8-8.252.09.1 +[00:17:19] [01] [00:08:10] Finished java/openjdk8 | openjdk8-8.252.09.1: Failed: build +[00:17:20] Stopping 4 builders +[00:17:21] Error: Depends failed to build +[00:17:21] Failed ports: java/openjdk8:build +[00:17:21] Cleaning up +[00:17:21] Unmounting file systems Added: head/biology/picard-tools/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/picard-tools/distinfo Sat Jun 13 13:54:47 2020 (r538672) @@ -0,0 +1,3 @@ +TIMESTAMP = 1591387929 +SHA256 (picard.jar) = a3d8830f68443a745cca9e1bab9adbc1c435fe3639709b118f5a89858a12a362 +SIZE (picard.jar) = 17520128 Added: head/biology/picard-tools/files/picard.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/picard-tools/files/picard.in Sat Jun 13 13:54:47 2020 (r538672) @@ -0,0 +1,14 @@ +#!/bin/sh -e + +if [ $# = 0 ] || [ $1 = -h ]; then + cat << EOM + +"picard" is a wrapper script around the Picard tools Java jar. + +To run Picard tools the traditional way, run + + java -jar %%JAVAJARDIR%%/picard.jar [args] + +EOM +fi +java -jar %%JAVAJARDIR%%/picard.jar "$@" Added: head/biology/picard-tools/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/picard-tools/pkg-descr Sat Jun 13 13:54:47 2020 (r538672) @@ -0,0 +1,5 @@ +Picard is a set of command line tools for manipulating high-throughput +sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file +formats are defined in the Hts-specs repository. + +WWW: https://broadinstitute.github.io/picard/
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