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| -rw-r--r-- | academic/aliview/README | 42 | ||||
| -rw-r--r-- | academic/aliview/References | 3 | ||||
| -rw-r--r-- | academic/aliview/aliview.SlackBuild | 13 | ||||
| -rw-r--r-- | academic/aliview/aliview.info | 6 |
4 files changed, 31 insertions, 33 deletions
diff --git a/academic/aliview/README b/academic/aliview/README index d9e65dc923..6d6a532cd1 100644 --- a/academic/aliview/README +++ b/academic/aliview/README @@ -1,36 +1,36 @@ AliView is yet another alignment viewer and editor, but this is probably one of the fastest and most intuitive to use. Features: -- fast and light-weight +- fast and light-weight - simple navigation, mouse-wheel zoom out and zoom in - highlight consensus characters or characters deviating - edit sequences/alignment (manually) -- align, add and align automatically with any aligner of your choice -- align new sequences to existing or realign all -- realign a selected block -- realign nucleotides as translated amino-acids -- delete vertical gaps -- undo/redo +- align, add and align automatically with any aligner of your choice +- align new sequences to existing or realign all +- realign a selected block +- realign nucleotides as translated amino-acids +- delete vertical gaps +- undo/redo - find degenerate primers in conserved regions in an alignment - open and save in FASTA, NEXUS, PHYLIP, CLUSTAL or MSF format -- print (current view) -- export whole alignment as an image file (png-format) -- copy selection (as fasta-sequences or just characters) -- paste sequences (as sequences or filenames) -- add more sequences from file +- print (current view) +- export whole alignment as an image file (png-format) +- copy selection (as fasta-sequences or just characters) +- paste sequences (as sequences or filenames) +- add more sequences from file - merge two sequences - and calculate consensus -- translate (view) nucleotide sequences as amino-acid sequences -- save translated alignment -- read / preserve Codonpos, Charset and Excludes (Nexus-specification) -- change Codonpos for selected regions (Nexus-specification) -- drag-drop/remove of sequences/files -- move sequences to top/bottom with key-stroke +- translate (view) nucleotide sequences as amino-acid sequences +- save translated alignment +- read / preserve Codonpos, Charset and Excludes (Nexus-specification) +- change Codonpos for selected regions (Nexus-specification) +- drag-drop/remove of sequences/files +- move sequences to top/bottom with key-stroke - a simple "external interface" that lets you invoke other programs - search function that finds patterns across gaps and follows IUPAC -- search multiple sequence names at once (stored in clipboard) -- reverse complement/reverse/complement sequences or whole alignment +- search multiple sequence names at once (stored in clipboard) +- reverse complement/reverse/complement sequences or whole alignment - different color schemes -- sort sequences by name +- sort sequences by name - sort sequences by residue in selected column Citation: diff --git a/academic/aliview/References b/academic/aliview/References new file mode 100644 index 0000000000..788ea92323 --- /dev/null +++ b/academic/aliview/References @@ -0,0 +1,3 @@ +Larsson, A. (2014). AliView: a fast and lightweight alignment viewer +and editor for large data sets. Bioinformatics30(22): 3276-3278. +http://dx.doi.org/10.1093/bioinformatics/btu531 diff --git a/academic/aliview/aliview.SlackBuild b/academic/aliview/aliview.SlackBuild index 12f023916d..dcd65c971b 100644 --- a/academic/aliview/aliview.SlackBuild +++ b/academic/aliview/aliview.SlackBuild @@ -23,18 +23,10 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=aliview -VERSION=${VERSION:-1.21} +VERSION=${VERSION:-1.23} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi - CWD=$(pwd) TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM @@ -51,6 +43,8 @@ rm -rf $PRGNAM-$VERSION mkdir $PRGNAM-$VERSION cd $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM.tgz +cd $PRGNAM + chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -73,6 +67,7 @@ cp aliicon_128x128.png $PKG/usr/share/pixmaps/$PRGNAM.png mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a install.readme.txt README.txt $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/aliview/aliview.info b/academic/aliview/aliview.info index f4241366de..2dc48d1e31 100644 --- a/academic/aliview/aliview.info +++ b/academic/aliview/aliview.info @@ -1,8 +1,8 @@ PRGNAM="aliview" -VERSION="1.21" +VERSION="1.23" HOMEPAGE="http://www.ormbunkar.se/aliview/" -DOWNLOAD="http://www.ormbunkar.se/aliview/downloads/linux/linux-version-1.21/aliview.tgz" -MD5SUM="9b04979a88a5cae94d9b1580e9aa2f7a" +DOWNLOAD="http://www.ormbunkar.se/aliview/downloads/linux/linux-versions-all/linux-version-1.23/aliview.tgz" +MD5SUM="b05a65ad2a70332343ef9ce6a28a9dcb" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="jdk" |