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author | 2021-02-20 21:30:34 +0100 | |
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committer | 2021-02-20 22:57:41 +0100 | |
commit | 9d417a388180071cd3607dd05447c20ccd789e21 (patch) | |
tree | e5e46435f24263dbca4677fd05870176f7dd3078 /sci-biology/tagdust | |
parent | sci-biology/subread: Fix build with gcc-10 (diff) | |
download | sci-9d417a388180071cd3607dd05447c20ccd789e21.tar.gz sci-9d417a388180071cd3607dd05447c20ccd789e21.tar.bz2 sci-9d417a388180071cd3607dd05447c20ccd789e21.zip |
sci-biology/tagdust: Port to EAPI 7
Closes: https://bugs.gentoo.org/755785
Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr>
Diffstat (limited to 'sci-biology/tagdust')
-rw-r--r-- | sci-biology/tagdust/files/tagdust-20101028-fno-common.patch | 77 | ||||
-rw-r--r-- | 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 } |