Date: Sun, 30 Aug 2020 06:55:33 +0400 From: Roman Bogorodskiy <bogorodskiy@gmail.com> To: "Jason W. Bacon" <jwb@freebsd.org> Cc: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: Re: svn commit: r538672 - in head/biology: . picard-tools picard-tools/files Message-ID: <20200830025523.GA1875@kloomba> In-Reply-To: <202006131354.05DDslB6089429@repo.freebsd.org> References: <202006131354.05DDslB6089429@repo.freebsd.org>
next in thread | previous in thread | raw e-mail | index | archive | help
--Y7xTucakfITjPcLV Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Jason W. Bacon wrote: > Author: jwb > Date: Sat Jun 13 13:54:47 2020 > New Revision: 538672 > URL: https://svnweb.freebsd.org/changeset/ports/538672 >=20 > Log: > biology/picard-tools: CLI tools for manipulating sequencing data > =20 > 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 f= ile > formats are defined in the Hts-specs repository. >=20 > Added: > head/biology/picard-tools/ > head/biology/picard-tools/Makefile (contents, props changed) > head/biology/picard-tools/buildlog-12-1-amd64-wip-picard-tools (conte= nts, props changed) ^^^^ =20 Is this buildlog really needed in the repo? > 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 >=20 > Modified: head/biology/Makefile > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D > --- 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 +=3D phred > SUBDIR +=3D phylip > SUBDIR +=3D phyml > + SUBDIR +=3D picard-tools > SUBDIR +=3D plink > SUBDIR +=3D primer3 > SUBDIR +=3D prodigal >=20 > Added: head/biology/picard-tools/Makefile > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D > --- /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=3D picard > +DISTVERSION=3D 2.22.9 > +CATEGORIES=3D biology java > +MASTER_SITES=3D http://github.com/broadinstitute/picard/releases/downloa= d/${PORTVERSION}/ > +PKGNAMESUFFIX=3D -tools > +DISTNAME=3D ${PORTNAME} > +EXTRACT_SUFX=3D .jar > + > +MAINTAINER=3D jwb@FreeBSD.org > +COMMENT=3D CLI tools for manipulating high-throughput sequencing (HTS) d= ata > + > +LICENSE=3D MIT > + > +RUN_DEPENDS=3D samtools:biology/samtools > + > +USE_JAVA=3D 1.8+ > +JAVA_RUN=3D yes > + > +SUB_FILES=3D picard > +NO_BUILD=3D yes > +NO_ARCH=3D yes > + > +PLIST_FILES=3D 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> >=20 > Added: head/biology/picard-tools/buildlog-12-1-amd64-wip-picard-tools > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D > --- /dev/null 00:00:00 1970 (empty, because file is newly added) > +++ head/biology/picard-tools/buildlog-12-1-amd64-wip-picard-tools Sat Ju= n 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-def= ault/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: 3.1.2019123= 1,1 > +[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= =2E13.1_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= =2E51 > +[00:00:11] Deleting libXdamage-1.1.5.txz: missing dependency: libX11-1.6= =2E9,1 > +[00:00:11] Deleting libXdmcp-1.1.3.txz: missing dependency: xorgproto-20= 19.2 > +[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= =2E6.9,1 > +[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-3.1.201= 91211,1 > +[00:00:11] Deleting mesa-libs-18.3.2_4.txz: missing dependency: libX11-1= =2E6.9,1 > +[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: Su= ccess > +[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: Succe= ss > +[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= =2E7.5 > +[00:01:30] [03] [00:00:03] Finished java/javavmwrapper | javavmwrapper-2= =2E7.5: 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: Su= ccess > +[00:02:12] [02] [00:00:00] Building java/java-zoneinfo | java-zoneinfo-2= 019.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-2= 019.b: Success > +[00:02:15] [02] [00:00:00] Building devel/libinotify | libinotify-201802= 01_1 > +[00:02:41] [02] [00:00:26] Finished devel/libinotify | libinotify-201802= 01_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: S= uccess > +[00:05:05] [01] [00:02:53] Finished x11/libX11 | libX11-1.6.9_1,1: Succe= ss > +[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: S= uccess > +[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: Succe= ss > +[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: Suc= cess > +[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: Succe= ss > +[00:06:21] [04] [00:04:19] Finished security/gnutls | gnutls-3.6.13: Suc= cess > +[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: S= uccess > +[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: Suc= cess > +[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 >=20 > Added: head/biology/picard-tools/distinfo > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D > --- /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 =3D 1591387929 > +SHA256 (picard.jar) =3D a3d8830f68443a745cca9e1bab9adbc1c435fe3639709b11= 8f5a89858a12a362 > +SIZE (picard.jar) =3D 17520128 >=20 > Added: head/biology/picard-tools/files/picard.in > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D > --- /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 (r= 538672) > @@ -0,0 +1,14 @@ > +#!/bin/sh -e > + > +if [ $# =3D 0 ] || [ $1 =3D -h ]; then > + cat << EOM > + > +"picard" is a wrapper script around the Picard tools Java jar. > + > +To run Picard tools the traditional way, run > + > + java -jar %%JAVAJARDIR%%/picard.jar [args] > + > +EOM > +fi > +java -jar %%JAVAJARDIR%%/picard.jar "$@" >=20 > Added: head/biology/picard-tools/pkg-descr > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D > --- /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 fi= le > +formats are defined in the Hts-specs repository. > + > +WWW: https://broadinstitute.github.io/picard/ Roman Bogorodskiy --Y7xTucakfITjPcLV Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQEzBAABCAAdFiEEi6TfKtFPmbY34ABwyW1f/gjCImoFAl9LFSUACgkQyW1f/gjC ImqRZgf+KtGGYpSQAmk+LxNnI7EL+d3t+uD0zQ6mDKIjfv/13ZOye7P2/OcxmMD0 QD0wNXBnuOI7VAsUDG/oRHl2utVVRy1sq7DPpavbNLDaDLR/B/6OmS2t7wbe0BBB mNACM0JJ+c0k2YK04iBVRYenOa2fbI6D+2qzMUQnewqB7zUkjez6B3YTRBExXdew /VlTgwm6jjeRYjj81hA69dtygGbcnVYGqKsPu1CYLFQxJu7pzaOTgvl+3Qw8HuE5 oDZy0P6MZ+fLNy7ZPg+T12Qjf+Hg4xk4OYi/BTzaWj/fLfLD9IZOxAGeid//+KbO IzIarANHHOwNmWyHgxBQfEWr67UcEQ== =8Kw3 -----END PGP SIGNATURE----- --Y7xTucakfITjPcLV--
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?20200830025523.GA1875>