Commit 433c0d2d authored by Afif Elghraoui's avatar Afif Elghraoui

Initial packaging

parent 02d8b73b
#!/bin/bash
selfdir="$(realpath ${BASH_SOURCE[0]})"
export PATH="$(realpath $selfdir/../share/assemblytics/bin):$PATH"
exec web_pipeline "$@"
.TH Assemblytics 1 "February 11 2018"
.\" Please adjust this date whenever revising the manpage.
.\"
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.\" .ad l left justify
.\" .ad b justify to both left and right margins
.\" .nf disable filling
.\" .fi enable filling
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.\" for manpage-specific macros, see man(7)
.SH NAME
Assemblytics \- detect and analyze structural variants from a genome assembly
.SH SYNOPSIS
.B Assemblytics
.I delta output_prefix unique_length_required min_size max_size
.SH DESCRIPTION
.B Assemblytics
incorporates a unique anchor filtering approach to increase
robustness to repetitive elements, and identifies six classes of variants
based on their distinct alignment signatures.
.B Assemblytics
can be applied both to comparing aberrant genomes, such as human cancers, to a reference, or to identify differences between related species.
.SH EXAMPLES
Generate the delta file with
.BR nucmer (1):
.RS 4
nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT
.RE
.sp 1
Then run the program:
.RS 4
Assemblytics OUT.delta OUT 10000 50 10000
.RE
.SH CITATION
Maria Nattestad, Michael C. Schatz; Assemblytics: a web analytics tool for the detection of variants from an assembly, Bioinformatics, Volume 32, Issue 19, 1 October 2016, Pages 3021–3023, https://doi.org/10.1093/bioinformatics/btw369
.SH SEE ALSO
.BR nucmer (1),
http://assemblytics.com
Assemblytics for Debian
----------------------
This program is available both as a web application [1-2] and as a
command-line tool [3]. However, the backend for the web application has
slightly diverged from the command-line version. Since they are so
similar, the source for the web backend is used here and patched
appropriately to reflect the command-line usage.
1. http://assemblytics.com/
2. https://github.com/MariaNattestad/Assemblytics_web
3. https://github.com/MariaNattestad/Assemblytics
-- Afif Elghraoui <afif@debian.org>, Sun, 11 Feb 2018 22:37:17 -0500
assemblytics (0~20170131+ds-1) UNRELEASED; urgency=medium
* Initial release (Closes: #890220)
-- Afif Elghraoui <afif@debian.org> Sun, 11 Feb 2018 18:53:57 -0500
Source: assemblytics
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Afif Elghraoui <afif@debian.org>
Build-Depends: debhelper (>= 11)
Standards-Version: 4.1.3
Homepage: http://assemblytics.com/
Vcs-Git: https://salsa.debian.org/med-team/assemblytics.git
Vcs-Browser: https://salsa.debian.org/med-team/assemblytics.git
Package: assemblytics
Architecture: all
Depends:
${misc:Depends},
perl,
python,
python-numpy,
r-base-core,
r-cran-ggplot2,
r-cran-plyr,
r-cran-rcolorbrewer,
Recommends: mummer
Description: detect and analyze structural variants from a genome assembly
Assemblytics incorporates a unique anchor filtering approach to increase
robustness to repetitive elements, and identifies six classes of variants
based on their distinct alignment signatures. Assemblytics can be applied
both to comparing aberrant genomes, such as human cancers, to a reference,
or to identify differences between related species.
debian/Assemblytics /usr/bin/
bin /usr/share/assemblytics/
debian/Assemblytics.1
Description: adapt web-backend for command-line usage
See debian/README.source
Author: Afif Elghraoui <afif@debian.org>
Forwarded: no
Last-Update: 2018-02-11
--- assemblytics.orig/bin/web_pipeline
+++ assemblytics/bin/web_pipeline
@@ -1,5 +1,5 @@
#!/bin/bash
-USAGE="web_pipeline delta output_prefix unique_length_required min_size"
+USAGE="Assemblytics delta output_prefix unique_length_required min_size max_size"
if [ -z "$1" ]
then
echo "ERROR in Assemblytics: No delta file given"
@@ -49,7 +49,7 @@
>&2 echo Input delta file: $DELTA
>&2 echo Output prefix: $OUTPUT_PREFIX
-LOG_FILE=${OUTPUT_PREFIX%/*}/progress.log
+LOG_FILE=/dev/stdout
echo "${OUTPUT_PREFIX##*/}" >> $LOG_FILE
@@ -94,8 +94,6 @@
./bin/Assemblytics_summary.py -i $OUTPUT_PREFIX.Assemblytics_structural_variants.bed -min $MINIMUM_SIZE -max $MAXIMUM_SIZE > $OUTPUT_PREFIX.Assemblytics_structural_variants.summary
- zip $OUTPUT_PREFIX.Assemblytics_results.zip $OUTPUT_PREFIX.Assemblytics*
- head $OUTPUT_PREFIX.Assemblytics_structural_variants.bed | column -t > $OUTPUT_PREFIX.variant_preview.txt
if grep -q "Total" $OUTPUT_PREFIX.Assemblytics_structural_variants.summary;
then
#!/usr/bin/make -f
libexec = debian/assemblytics/usr/share/assemblytics/bin
%:
dh $@
override_dh_install:
dh_install
sed -ri 's|(Rscript\s+)?\./bin/||' $(libexec)/web_pipeline
sed -ri '1s|^#!\s*/usr/bin/env\s+|#!/usr/bin/|' $(libexec)/*
sed -i '1s|^|#!/usr/bin/Rscript\n|' $(libexec)/*.R
override_dh_fixperms:
chmod +x $(libexec)/*
dh_fixperms
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