diff --git a/debian/README.Debian b/debian/README.Debian index 23e0757..700b230 100644 --- a/debian/README.Debian +++ b/debian/README.Debian @@ -11,6 +11,13 @@ In version 2.13-1, the binaries and man pages all have a prefix "tigr-" to avoid conflicts with other programs, with extract in particular. -This was changed +This was changed in the current packaging of version 3.x in favour of +putting the executables under /usr/lib/tigr-glimmer. A wrapper is +provided that enables to call the binaries via + + tigr-glimmer + +(see man tigr-glimmer). Alternatively you might add this directory +to your search PATH to call the binaries directly. -- Steffen Moeller , Thu, 10 Nov 2004 12:33:46 +0100 diff --git a/debian/bin/tigr-glimmer b/debian/bin/tigr-glimmer new file mode 100644 index 0000000..91e5ba9 --- /dev/null +++ b/debian/bin/tigr-glimmer @@ -0,0 +1,24 @@ +#!/bin/sh + +BINDIR=/usr/lib/tigr-glimmer + +if [ $# -lt 1 ] ; then + echo "Usage: $0 " 1>&2 + echo " Existing programs are:" + ls ${BINDIR} + exit 1 +fi + +WRAPPER=$0 +PROGRAM=$1 +shift +ARGS=$* + +if [ -x ${BINDIR}/${PROGRAM} ]; then + exec ${BINDIR}/${PROGRAM} ${ARGS} +else + echo "Usage: ${PROGRAM} does not exist in Tigr Glimmer" + echo " Existing programs are:" + ls ${BINDIR} + exit 1 +fi diff --git a/debian/bin/tigr-run-glimmer3 b/debian/bin/tigr-run-glimmer3 new file mode 100755 index 0000000..e74a5c8 --- /dev/null +++ b/debian/bin/tigr-run-glimmer3 @@ -0,0 +1,18 @@ +#!/bin/sh +echo "run Glimmer3" +clear +echo "Genome is " $1 +echo "Find non-overlapping orfs in tmp.coord" +BINDIR="/usr/lib/tigr-glimmer" +rm -f tmp.coord +${BINDIR}/long-orfs $1 | ${BINDIR}/get-putative >tmp.coord +echo "Extract training sequences to tmp.train" +rm -f tmp.train +${BINDIR}/extract $1 tmp.coord >tmp.train +wc tmp.train +echo "Build interpolated context model in tmp.model" +rm -f tmp.model +${BINDIR}/build-icm tmp.model +echo "Predict genes with Glimmer3 with coordinates in g3.coord" +rm -f g3.coord +${BINDIR}/glimmer3 $1 tmp.model | ${BINDIR}/get-putative >g3.coord diff --git a/debian/index.html b/debian/index.html deleted file mode 100644 index f4bd0f6..0000000 --- a/debian/index.html +++ /dev/null @@ -1,168 +0,0 @@ - -EXTRACT

EXTRACT

Name

extract -- Fine start/stop positions of genes in genome sequence

Synopsis

long-orgs [genome-file options]

DESCRIPTION

Program extract takes a FASTA format sequence file and a file -with a list of start/stop positions in that file (e.g., as produced -by the long-orfs program) and extracts and outputs the -specified sequences.

The first command-line argument is the name of the sequence file, -which must be in FASTA format.

The second command-line argument is the name of the coordinate file. -It must contain a list of pairs of positions in the first file, one -per line. The format of each entry is:

<IDstring>> <start position> <stop position>

This file should contain no other information, so if you're using -the output of glimmer or long-orfs , you'll have to cut off -header lines.

The output of the program goes to the standard output and has one -line for each line in the coordinate file. Each line contains -the IDstring , followed by white space, followed by the substring -of the sequence file specified by the coordinate pair. Specifically, -the substring starts at the first position of the pair and ends at -the second position (inclusive). If the first position is bigger -than the second, then the DNA reverse complement of each position -is generated. Start/stop pairs that "wrap around" the end of the -genome are allowed.

OPTIONS

-skip

makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of the previous version of the program.

-l

makes the output omit an sequences shorter than n characters. - n includes the 3 skipped characters if the -skip switch - is one. -

SEE ALSO

glimmer2 (1), -long-orfs (1), -adjust (1), -anomaly (1), -build-icm (1), -check (1), -codon-usage (1), -compare-lists (1), -extract (1), -generate (1), -get-len (1), -get-putative (1),

http://www.tigr.org/software/glimmer/

Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.

AUTHOR

This manual page was quickly copied from the glimmer web site by Steffen Moeller <moeller@pzr.uni-rostock.de> for - the Debian system. -

\ No newline at end of file diff --git a/debian/install b/debian/install index 6d10f8b..e8750d7 100644 --- a/debian/install +++ b/debian/install @@ -1,3 +1,2 @@ bin/* usr/lib/tigr-glimmer -debian/tigr-run-glimmer3 usr/bin -debian/tigr-glimmer usr/bin +debian/bin/* usr/bin diff --git a/debian/tigr-glimmer b/debian/tigr-glimmer deleted file mode 100644 index 91e5ba9..0000000 --- a/debian/tigr-glimmer +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/sh - -BINDIR=/usr/lib/tigr-glimmer - -if [ $# -lt 1 ] ; then - echo "Usage: $0 " 1>&2 - echo " Existing programs are:" - ls ${BINDIR} - exit 1 -fi - -WRAPPER=$0 -PROGRAM=$1 -shift -ARGS=$* - -if [ -x ${BINDIR}/${PROGRAM} ]; then - exec ${BINDIR}/${PROGRAM} ${ARGS} -else - echo "Usage: ${PROGRAM} does not exist in Tigr Glimmer" - echo " Existing programs are:" - ls ${BINDIR} - exit 1 -fi diff --git a/debian/tigr-run-glimmer3 b/debian/tigr-run-glimmer3 deleted file mode 100755 index e74a5c8..0000000 --- a/debian/tigr-run-glimmer3 +++ /dev/null @@ -1,18 +0,0 @@ -#!/bin/sh -echo "run Glimmer3" -clear -echo "Genome is " $1 -echo "Find non-overlapping orfs in tmp.coord" -BINDIR="/usr/lib/tigr-glimmer" -rm -f tmp.coord -${BINDIR}/long-orfs $1 | ${BINDIR}/get-putative >tmp.coord -echo "Extract training sequences to tmp.train" -rm -f tmp.train -${BINDIR}/extract $1 tmp.coord >tmp.train -wc tmp.train -echo "Build interpolated context model in tmp.model" -rm -f tmp.model -${BINDIR}/build-icm tmp.model -echo "Predict genes with Glimmer3 with coordinates in g3.coord" -rm -f g3.coord -${BINDIR}/glimmer3 $1 tmp.model | ${BINDIR}/get-putative >g3.coord