blob: d4b19252c86f85af612901687bef2a8683b3d023 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
|
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=3
inherit python java-pkg-2
DESCRIPTION="Graphical viewer for next generation sequence assemblies and alignments."
HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
SRC_URI="http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_1_11_02_18.sh
http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
# Tablet uses a modified version of the BSD License which has been edited to remove
# references to distribution and use in source forms. This means that we are happy
# for you to distribute and use Tablet however you please, but we do not (yet) want
# to make the source code publicly available.
# It's in the installer, and ends up on disk after installation at /opt/Tablet/docs/tablet.html
# The original BSD licence was modified to remove references to distribution and use in
# source forms, because we cannot make the source code available for Tablet.
LICENSE="Tablet"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
virtual/jre
dev-lang/python"
src_install() {
# In theory it seems this binary package could be installed through ant instead
# of the install4j package which is not easy to be forced non-interactive.
# The below approach is not ideal.
sed "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile > "${DISTDIR}"/response.varfile || die "sed failed"
# the intallation script somehow does not pickup
# -varfile="${DISTDIR}"/response.varfile from the commandline and tehrefore
# we place the file rather directly into the place where it should reside.
# In the file you can read details how the variables were mangled. For
# example, the trick with sys.symlinkDir in the response.varfile is to
# disable the installation process to symlink from /usr/local/bin/table to
# /opt/Tablet/tablet. That was logged in that file with the following line:
#
# /scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String]
#
# The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile
mkdir -p "${D}"/opt/Tablet/.install4j || die "Cannot pre-create "${D}"/opt/Tablet/.install4j/"
cat "${DISTDIR}"/response.varfile > "${D}"/opt/Tablet/.install4j/response.varfile || die "Cannot write "${D}"/opt/Tablet/.install4j/response.varfile"
# make sure we force java to point a to $HOME which is inside our sanbox
# directory area. We force -Duser.home . It seems also -Dinstall4j.userHome
# could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/
sed "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${D}"/../temp -Dinstall4j.jvmDir#" -i "${DISTDIR}"/tablet_linux_x86_1_11_02_18.sh || die "failed to set userHome value"
sh "${DISTDIR}"/tablet_linux_x86_1_11_02_18.sh -q -overwrite -varfile="${DISTDIR}"/response.varfile --destination="${D}"/opt/Tablet -dir /scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet
dobin "${DISTDIR}"/coveragestats.py
}
|
GitWeb
