[gentoo-commits] proj/sci:master commit in: sci-biology/fsl/, sci-biology/fsl/files/

[Justin Lecher]

commit:     eda8f3c599b7c146c971ba0295235a99604062b8
Author:     Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Wed Jan  4 11:13:11 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan  4 11:13:11 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=eda8f3c5

sci-biology/fsl: fixed outstanding FSLDIR and GUI issues (#716)

* sci-biology/fsl: addressing FSLDIR via symlinks

* sci-biology/fsl: fixed FSL GUI

Package-Manager: Portage-2.3.3, Repoman-2.3.1

* sci-biology/fsl: EAPI update

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/fsl/files/99fsl      |  2 +-
 sci-biology/fsl/fsl-5.0.8.ebuild | 11 +++++++++--
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/sci-biology/fsl/files/99fsl b/sci-biology/fsl/files/99fsl
index ca37941..41db5c5 100644
--- a/sci-biology/fsl/files/99fsl
+++ b/sci-biology/fsl/files/99fsl
@@ -2,4 +2,4 @@ FSLOUTPUTTYPE=NIFTI_GZ
 FSLMULTIFILEQUIT=TRUE
 FSLTCLSH=tclsh
 FSLWISH=wish
-FSLDIR=/usr
+FSLDIR=/usr/share/fsl

diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index 3e9dc99..f6e57d1 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 inherit eutils toolchain-funcs prefix
 
@@ -87,6 +87,7 @@ src_prepare(){
                $(grep -rl "\'\${FSLDIR}\'/doc" src/*)
 
        sed -i -e "s:\$FSLDIR/etc:/etc:g" `grep -rlI \$FSLDIR/etc *`
+       default
 }
 
 src_compile() {
@@ -127,6 +128,12 @@ src_install() {
        #       doins etc/matlab
        #fi
 
+       #the following is needed for FSL and depending programs to be able
+       #to find its files, since FSL uses an uncommon:
+       #https://github.com/gentoo-science/sci/pull/612#r60289295
+       dosym /etc /usr/share/fsl/etc
+       dosym /usr/share/doc/${P} /usr/share/fsl/doc
+
        doenvd "${FILESDIR}"/99fsl
        mv "${ED}"/usr/bin/{,fsl_}cluster || die
 }