[gentoo-commits] proj/sci:master commit in: sci-biology/symap/

[Andrew Ammerlaan]

commit:     4d0370cad9584f28fe77059521a641287a501d88
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Feb  4 07:45:17 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Feb  4 07:45:17 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4d0370ca

sci-biology/symap: version bump, EAIP bump

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/symap/symap-4.0.ebuild   | 29 --------------------------
 sci-biology/symap/symap-5.0.6.ebuild | 40 ++++++++++++++++++++++++++++++++++++
 2 files changed, 40 insertions(+), 29 deletions(-)

diff --git a/sci-biology/symap/symap-4.0.ebuild b/sci-biology/symap/symap-4.0.ebuild
deleted file mode 100644
index bc485ff04..000000000
--- a/sci-biology/symap/symap-4.0.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Synteny Mapping and Analysis Program"
-HOMEPAGE="http://www.agcol.arizona.edu/software/symap/"
-SRC_URI="symap_40.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-#KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	elog "Please register and download symap_${PV}.tar.gz (110MB)"
-	elog "at http://www.agcol.arizona.edu/software/symap/v${PV}/download/"
-	elog "and place it in ${DISTDIR}"
-}
-
-DEPEND="
-	sci-biology/blat
-	sci-biology/mummer
-	sci-biology/muscle"
-RDEPEND="${DEPEND}
-	virtual/jre"

diff --git a/sci-biology/symap/symap-5.0.6.ebuild b/sci-biology/symap/symap-5.0.6.ebuild
new file mode 100644
index 000000000..58b444b3d
--- /dev/null
+++ b/sci-biology/symap/symap-5.0.6.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Synteny Mapping and Analysis Program"
+HOMEPAGE="http://www.agcol.arizona.edu/software/symap/ https://github.com/csoderlund/SyMAP"
+SRC_URI="https://github.com/csoderlund/SyMAP/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+# error: package netscape.javascript does not exist
+KEYWORDS=""
+
+DEPEND="
+	sci-biology/blat
+	sci-biology/mummer
+	sci-biology/muscle"
+RDEPEND="${DEPEND}
+	>=virtual/jre-1.7:*"
+
+S="${WORKDIR}/SyMAP-${PV}/java"
+
+src_unpack() {
+	default
+	cd "${S}"
+	tar xvf classes_ext.tar.gz
+	cd ../
+	tar xvf ext.tar.gz
+}
+
+src_prepare() {
+	default
+	sed -e 's/#JAVA_PATH=\/usr/JAVA_PATH=\/usr/g' -i Makefile || die
+}
+
+src_compile() {
+	emake class_dirs
+	emake
+}