diff options
| author | BioArchLinuxBot | 2024-06-04 03:42:17 +0000 |
|---|---|---|
| committer | BioArchLinuxBot | 2024-06-04 03:42:17 +0000 |
| commit | fa8b59ef0a1a8a350f20612218d3baeef575b596 (patch) | |
| tree | 57dbf5539320b930ad90d83c20eee541ef900a4a /PKGBUILD | |
| parent | 853010de91b00b6831744ad4a9be9ac896d030dd (diff) | |
| download | aur-trinityrnaseq.tar.gz | |
[lilac] updated to 2.15.1-2
Diffstat (limited to 'PKGBUILD')
| -rw-r--r-- | PKGBUILD | 41 |
1 files changed, 20 insertions, 21 deletions
@@ -4,7 +4,7 @@ basename=trinityrnaseq pkgname=('trinityrnaseq' 'trinityrnaseq-doc' 'trinityrnaseq-extra') _pkgname=Trinity pkgver=2.15.1 -pkgrel=1 +pkgrel=2 pkgdesc="Transcriptome assembler for RNA-seq reads \ https://doi.org/10.1038%2Fnbt.1883" url="https://github.com/Trinotate/Trinotate/wiki" @@ -13,7 +13,7 @@ arch=('x86_64') makedepends=('git' 'cmake' 'make' 'python' 'rsync') source=("git+https://github.com/trinityrnaseq/trinityrnaseq.git#tag=$_pkgname-v$pkgver" "string.patch") -sha256sums=('SKIP' +sha256sums=('3764a52e34eacdf4affc1ab719901e90c68e326b9be7b70a8bacdb8843e0aedf' '9304eae411d76a6ce1846ed06e7311b35175638a74ec6277909ef9d4ba71769b') prepare(){ @@ -31,16 +31,15 @@ build() { package_trinityrnaseq() { depends=('perl' 'bash' 'glibc' 'java-runtime' 'python' 'zlib') # 'xz' 'bzip2' 'curl' - - cd $srcdir/$basename - mkdir -p $pkgdir/usr/{share/{$pkgname,java},bin} - - ls + set -x + cd $srcdir/trinityrnaseq + mkdir -p $pkgdir/usr/{share/{trinityrnaseq,java},bin} # Dir for dir in Analysis PerlLib PyLib do - find $dir -type f -exec install -D -m 755 {} $pkgdir/usr/share/$basename/$dir \; + mkdir -p $pkgdir/usr/share/trinityrnaseq/$dir + find $dir -type f -exec install -D -m 755 {} $pkgdir/usr/share/trinityrnaseq/$dir \; done # Bin @@ -49,11 +48,12 @@ do find $binadir -type f -exec install -D -m 755 {} $pkgdir/usr/bin/ \; done - install -Dm755 Trinity $pkgdir/usr/bin/Trinity + install -Dm755 Trinity $pkgdir/usr/share/trinityrnaseq/Trinity + ln -s /usr/share/trinityrnaseq/Trinity $pkgdir/usr/bin/Trinity install -Dm755 trinity-plugins/BIN/seqtk-trinity $pkgdir/usr/bin/seqtk-trinity # Java - install -Dm755 Butterfly/Butterfly.jar $pkgdir/usr/share/Butterfly.jar + install -Dm755 Butterfly/Butterfly.jar $pkgdir/usr/share/java/Butterfly.jar # Plugin # Todo: check trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs @@ -67,35 +67,34 @@ done ) for plugin in "${plugins[@]}" do - ls $srcdir/$basename/$plugin - install -Dm755 $srcdir/$basename/$plugin $pkgdir/usr/share/$pkgname/$plugin + install -Dm755 $srcdir/trinityrnaseq/$plugin $pkgdir/usr/share/$pkgname/$plugin done - # Util - find util -type f -exec install -D -m 755 {} $pkgdir/usr/share/$basename/util \; + mkdir -p $pkgdir/usr/share/trinityrnaseq/util + find util -type f -exec install -D -m 755 {} $pkgdir/usr/share/trinityrnaseq/util \; } package_trinityrnaseq-doc(){ - cd $srcdir/$basename - mkdir -p $pkgdir/usr/share/doc/$basename/wiki + cd $srcdir/trinityrnaseq + mkdir -p $pkgdir/usr/share/doc/trinityrnaseq/wiki for note in developer.notes Changelog.txt README README.md do - install -Dm644 $note $pkgdir/usr/share/doc/$basename/$note + install -Dm644 $note $pkgdir/usr/share/doc/trinityrnaseq/$note done - find trinityrnaseq.wiki -type f -exec install -D -m 644 {} $pkgdir/usr/share/doc/$basename/wiki \; + find trinityrnaseq.wiki -type f -exec install -D -m 644 {} $pkgdir/usr/share/doc/trinityrnaseq/wiki \; } package_trinityrnaseq-extra(){ depends=('bash' 'perl') - cd $srcdir/$basename - mkdir -p $pkgdir/usr/share/$basename/{trinity_ext_sample_data,sample_data} + cd $srcdir/trinityrnaseq + mkdir -p $pkgdir/usr/share/trinityrnaseq/{trinity_ext_sample_data,sample_data} for datadir in trinity_ext_sample_data sample_data do - find $datadir -type f -exec install -D -m 755 {} $pkgdir/usr/share/$basename/$datadir/ \; + find $datadir -type f -exec install -D -m 755 {} $pkgdir/usr/share/trinityrnaseq/$datadir/ \; done } |