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

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

[Jakov Smolić]

commit:     9d417a388180071cd3607dd05447c20ccd789e21
Author:     Jakov Smolic <jakov.smolic <AT> sartura <DOT> hr>
AuthorDate: Sat Feb 20 20:30:34 2021 +0000
Commit:     Jakov Smolić <jakov.smolic <AT> sartura <DOT> hr>
CommitDate: Sat Feb 20 21:57:41 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9d417a38

sci-biology/tagdust: Port to EAPI 7

Closes: https://bugs.gentoo.org/755785
Signed-off-by: Jakov Smolic <jakov.smolic <AT> sartura.hr>

 .../files/tagdust-20101028-fno-common.patch        | 77 ++++++++++++++++++++++
 sci-biology/tagdust/tagdust-20101028.ebuild        | 17 +++--
 2 files changed, 85 insertions(+), 9 deletions(-)

diff --git a/sci-biology/tagdust/files/tagdust-20101028-fno-common.patch b/sci-biology/tagdust/files/tagdust-20101028-fno-common.patch
new file mode 100644
index 000000000..01fd2d274
--- /dev/null
+++ b/sci-biology/tagdust/files/tagdust-20101028-fno-common.patch
@@ -0,0 +1,77 @@
+--- a/background.c
++++ b/background.c
+@@ -28,6 +28,9 @@
+ #include <ctype.h>
+ #define MIN(a, b) (a > b ? b : a)
+ 
++extern int *seed;
++extern int nuc_code[255];
++
+ /*
+  
+  Collects length and nucleotide composition of the input reads. Simultaneously counts how many sequences are covered by x,x+1 ... percent library sequences
+--- a/detect.h
++++ b/detect.h
+@@ -70,11 +70,11 @@ struct stats_dat{
+ 	int *p_counts;
+ };
+ 
+-int nuc_code[255]; 
++extern int nuc_code[255]; 
+ 
+-int *seed;
++extern int *seed;
+ 
+-int linewrap;
++extern int linewrap;
+ 
+ void init_nuc_code();
+ 
+--- a/input.c
++++ b/input.c
+@@ -28,6 +28,10 @@
+ #include <ctype.h>
+ 
+ static int numseq = 0;
++extern int linewrap;
++extern int *seed;
++extern int nuc_code[255];
++
+ 
+ 
+ int compare(const void* a, const void* b)
+--- a/interface.c
++++ b/interface.c
+@@ -33,6 +33,8 @@
+ #define OPT_FASTA 5
+ #define OPT_MODEL 6
+ 
++extern int linewrap;
++
+ struct parameters* interface(struct parameters* param,int argc, char **argv)
+ {
+ 	int c;
+--- a/main.c
++++ b/main.c
+@@ -27,6 +27,10 @@
+ #include "detect.h"
+ #include "sys/time.h"
+ 
++int linewrap;
++int *seed;
++int nuc_code[255];
++
+ 
+ int main (int argc, char * argv[]) {
+ 	struct parameters* param = 0;
+--- a/test_sequence.c
++++ b/test_sequence.c
+@@ -26,6 +26,8 @@
+ 
+ #include "detect.h"
+ 
++extern int *seed;
++
+ /* 
+  Checks if a sequence is covered by library sequences. Return the fraction of residues covered by library sequences.  
+ */

diff --git a/sci-biology/tagdust/tagdust-20101028.ebuild b/sci-biology/tagdust/tagdust-20101028.ebuild
index 1357a0da5..2f5a1777e 100644
--- a/sci-biology/tagdust/tagdust-20101028.ebuild
+++ b/sci-biology/tagdust/tagdust-20101028.ebuild
@@ -1,7 +1,7 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="Trim multimers of various primers/adapter from Illumina datasets"
 HOMEPAGE="http://genome.gsc.riken.jp/osc/english/dataresource"
@@ -10,23 +10,22 @@ SRC_URI="http://genome.gsc.riken.jp/osc/english/software/src/tagdust.tgz -> ${P}
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}"
+S="${WORKDIR}/tagdust"
 
-S="${WORKDIR}"/tagdust
+PATCHES=( "${FILESDIR}"/${P}-fno-common.patch )
 
 src_prepare(){
+	default
 	sed -e "s/^CFLAGS/#CFLAGS/" -e "s#/usr/local/bin#\$(DESTDIR)/usr/bin#" \
-		-e "s#/usr/share/man/#\$(DESTDIR)/usr/share/man/#" -i Makefile
+		-e "s#/usr/share/man/#\$(DESTDIR)/usr/share/man/#" -i Makefile || die
 }
 
-src_install(){
+src_install() {
 	doman tagdust.1
 	dobin tagdust
 	insinto /usr/share/tagdust/Illumina
-	doins "test/"solexa*.fa
+	doins test/solexa*.fa
 	insinto /usr/share/tagdust
-	doins "test/"protocol.txt README
+	doins test/protocol.txt README
 }