Date: Mon, 19 Apr 2021 11:03:42 +0200 From: Mathieu Arnold <mat@freebsd.org> To: Mateusz Piotrowski <0mp@freebsd.org> Cc: "Jason W. Bacon" <jwb@freebsd.org>, ports-committers@freebsd.org, dev-commits-ports-all@freebsd.org, dev-commits-ports-main@freebsd.org Subject: Re: git: 5164d38ee538 - main - biology/snpeff: Genetic variant annotation and effect prediction toolbox Message-ID: <20210419090342.bc5hep4f3wyggql6@aching.in.mat.cc> In-Reply-To: <5fffb95d-f470-6fe3-936e-7bd34f09e9be@FreeBSD.org> References: <202104181847.13IIl8nX040293@gitrepo.freebsd.org> <5fffb95d-f470-6fe3-936e-7bd34f09e9be@FreeBSD.org>
next in thread | previous in thread | raw e-mail | index | archive | help
--2hv4mbuaqtb7nbo5 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Sun, Apr 18, 2021 at 09:27:59PM +0200, Mateusz Piotrowski wrote: > Hi! >=20 > On 18/04/2021 20:47, Jason W. Bacon wrote: > > The branch main has been updated by jwb: > >=20 > > URL: https://cgit.FreeBSD.org/ports/commit/?id=3D5164d38ee538f6791a25b8= 1f28a27126b90444f7 > >=20 > > commit 5164d38ee538f6791a25b81f28a27126b90444f7 > > Author: Jason W. Bacon <jwb@FreeBSD.org> > > AuthorDate: 2021-04-18 18:46:14 +0000 > > Commit: Jason W. Bacon <jwb@FreeBSD.org> > > CommitDate: 2021-04-18 18:46:29 +0000 > >=20 > > biology/snpeff: Genetic variant annotation and effect prediction t= oolbox > [snip] > > diff --git a/biology/snpeff/Makefile b/biology/snpeff/Makefile > > new file mode 100644 > > index 000000000000..3973e9a9a792 > > --- /dev/null > > +++ b/biology/snpeff/Makefile > > @@ -0,0 +1,41 @@ > > +PORTNAME=3D snpeff > > +DISTVERSION=3D 5.0 > > +CATEGORIES=3D biology java python > > +MASTER_SITES=3D https://snpeff.blob.core.windows.net/versions/ > > +DISTNAME=3D snpEff_latest_core > Since DISTNAME is not unique you may consider setting DIST_SUBDIR. not may, must. > > + > > +do-install: > > + ${MKDIR} ${STAGEDIR}${JAVAJARDIR}/snpeff > > + ${MKDIR} ${STAGEDIR}${LIBEXEC_DIR} > > + ${INSTALL_SCRIPT} ${WRKSRC}/scripts/snpEff ${STAGEDIR}${PREFIX}/bin > > + ${INSTALL_SCRIPT} ${WRKSRC}/scripts/snpSift ${STAGEDIR}${PREFIX}/bin > > + ${INSTALL_DATA} ${WRKSRC}/*.jar ${STAGEDIR}${JAVAJARDIR}/snpeff > > + ${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 ${WRKSRC}/scripts/snpSift > A minor style issue: the targets are out of order. > > + > > +.include <bsd.port.mk> > [snip] > > --- /dev/null > > +++ b/biology/snpeff/files/patch-scripts_snpEff > > @@ -0,0 +1,27 @@ > > +--- scripts/snpEff.orig 2021-04-13 22:55:13 UTC > > ++++ scripts/snpEff > > +@@ -13,9 +13,10 @@ > > + # Created by: Brad Chapman > > + #--------------------------------------------------------------------= ------------------------------- > > + > > +-jardir=3D"$(cd "$(dirname "$0")" && cd ".." && pwd -P)" > > ++jardir=3D%%JAVAJARDIR%%/snpeff > > ++userdir=3D~/snpEff > > ++JAVA_HOME=3D%%PREFIX%%/openjdk12 >=20 > This should probably be LOCALBASE instead of PREFIX. Also, it's probably > better to just pass JAVA_HOME to REINPLACE_CMD (as currently this port is > going to break if it uses a Java version other than OpenJDK 12 (and the > Makefile specifies 12+). >=20 > Cheers, >=20 > Mateusz >=20 >=20 >=20 >=20 --=20 Mathieu Arnold --2hv4mbuaqtb7nbo5 Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQKTBAABCgB9FiEEVhwchfRfuV0unqO5KesJApEdfgIFAmB9R2pfFIAAAAAALgAo aXNzdWVyLWZwckBub3RhdGlvbnMub3BlbnBncC5maWZ0aGhvcnNlbWFuLm5ldDU2 MUMxQzg1RjQ1RkI5NUQyRTlFQTNCOTI5RUIwOTAyOTExRDdFMDIACgkQKesJApEd fgL24g/9GLCEgYIGDBLSbGOUQScYOpNB8LUfIqZFQx54jDZA7HgpppW5UqCT/ZHE KqEYFDvvGrJBjbsJipmBaTQHh8ksG4QEnOBOkOGrQEh4ff+Ln80ok2aABARPhbi1 myi0DPgbzSgmuKGWprECnJNAI4c2+5oFVXV3r/Z6vsMjenkwXbpUps4qHeQpYOII fOJJ708sBXC3E0upisOLv/75RlrzIHcusXl9G1S6mVl/2vVy1TAPxmxE992hMWm6 seQOXmQFgfYykXhEIm6wAYtEVhaE17xJIF6jsUxABPj7m09BihDrwsDvc8TpM7T2 WYfeWVNac4YnjrUxoutDPmzzU3rhrhMt3MmyBvqBaxF4AQeSgCdIMfYeNn9/LnTL g51qC8HFf7Wu4+8ciJ1jYJ+W9GIeNgGWe0V/gZZwHUk9eeGu4PiW8cY8USR+6cUA 7tz5408yH/xMbHPxssHw7nqdKLTJYK7fR7FMP+ld8innZj/4+hmB5lZKrzWFL+xX HL2wkTV0cbrti4fx6I3hvi/2nt+SPks7BpXZfKyVK+tbl5ptCi/2ir9Q4DvQOBL6 hHtJ6/3gGGQoHv+t3KSmjl9loKPUrKfWIcQdza+o5YaHm3erVV94gt5Q/LIB6yFX HPGCffx5A9suaO2JkOZB4LAXZDG+sILycqXdYg7Iyxv/1wKmInY= =RtPn -----END PGP SIGNATURE----- --2hv4mbuaqtb7nbo5--
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?20210419090342.bc5hep4f3wyggql6>