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debian/changelog
View file @ 822eeb78
phast (1.4+dfsg-2) UNRELEASED; urgency=medium
* Fix homepage
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Run part or the test suite
-- Andreas Tille <tille@debian.org> Thu, 18 Oct 2018 18:16:40 +0200
phast (1.4+dfsg-1) unstable; urgency=medium
* Initial release (Closes: #875555)
......
debian/control
View file @ 822eeb78
......@@ -3,16 +3,16 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
Build-Depends: debhelper (>= 11~),
liblapack-dev,
libblas-dev,
libtmglib-dev,
libpcre3-dev,
help2man
Standards-Version: 4.1.0
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/phast.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/phast.git
Homepage: http://compgen.cshl/edu/phast
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/phast
Vcs-Git: https://salsa.debian.org/med-team/phast.git
Homepage: http://compgen.cshl.edu/phast/
Package: phast
Architecture: any
......
debian/copyright
View file @ 822eeb78
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: PHAST
Upstream-Contact: Ritika Ramani <rramani@cshl.edu>
Source: https://github.com/CshlSiepelLab/phast/releases
......@@ -9,11 +9,11 @@ Comment: The file LICENSE.txt mentions Philip Hazel (University of Cambridge
the upstream source it is not mentioned here in this file.
Files: *
Copyright: 2002-2015 University of California, Cornell University
Copyright: 2002-2018 University of California, Cornell University
License: BSD-3-clause
Files: debian/*
Copyright: 2016 Andreas Tille <tille@debian.org>
Copyright: 2016-2018 Andreas Tille <tille@debian.org>
License: BSD-3-clause
License: BSD-3-clause
......
debian/patches/fix_test_makefile.patch 0 → 100644
View file @ 822eeb78
Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 18 Oct 2018 18:16:40 +0200
Description: Test suite makefile has syntax errors and there
was at least one buggy data file which was fixed.
.
With these changes `make msa_view` works but other targets are
throwing errors. This needs to be investigated
--- a/test/Makefile
+++ b/test/Makefile
@@ -7,30 +7,30 @@ all: msa_view phyloFit phastCons
msa_view:
@echo "*** Testing msa_view ***"
msa_view hmrc.ss -i SS --end 10000 > hmrc.fa
- @if [[ -n `diff --brief hmrc.fa hmrc_correct.fa` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa -o PHYLIP > hmrc.ph
msa_view hmrc.ph -i PHYLIP > hmrc.fa
- @if [[ -n `diff --brief hmrc.fa hmrc_correct.fa` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm
msa_view hmrc.mpm --in-format MPM > hmrc.fa
- @if [[ -n `diff --brief hmrc.fa hmrc_correct.fa` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa -o SS > hmrc_short_a.ss
msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss
- @if [[ -n `diff --brief hmrc_short_[ab].ss` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi
msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa
msa_view --seqs human,cow hmrc.fa > hm_b.fa
- @if [[ -n `diff --brief hm_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa
msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa
- @if [[ -n `diff --brief hmrc_nogaps_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa
msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa
- @if [[ -n `diff --brief hm_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa
msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa
- @if [[ -n `diff --brief hmrc_sub_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --summary -i SS > hmrc_summary
- @if [[ -n `diff --brief hmrc_summary hmrc_summary_correct` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi
@echo -e "Passed all tests.\n"
@rm -f hmrc.ph hmrc.fa hmrc.mpm hmrc_short_[ab].ss hm_[ab].fa hmrc_nogaps_[ab].fa hmrc_sub_[ab].fa hmrc_summary
@@ -43,40 +43,40 @@ msa_view:
phyloFit:
@echo "*** Testing phyloFit ***"
phyloFit hmrc.ss --subst-mod JC69 --tree "(human, (mouse,rat), cow)" -i SS --quiet
- @if [[ -n `diff --brief phyloFit.mod jc.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod jc.mod ; then echo "Rounding errors found" ; diff -u phyloFit.mod jc.mod ; fi
phyloFit hmrc.ss --subst-mod JC69 --tree "((((human,chimp), (mouse,rat)), cow), chicken)" -i SS --quiet
- @if [[ -n `diff --brief phyloFit.mod jc.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod jc.mod ; then echo "ERROR" ; exit 1 ; fi
phyloFit hmrc.ss --subst-mod F81 --tree "(human, (mouse,rat), cow)" -i SS --quiet
- @if [[ -n `diff --brief phyloFit.mod f81.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod f81.mod ; then echo "ERROR" ; exit 1 ; fi
phyloFit hmrc.ss --subst-mod HKY85 --tree "(human, (mouse,rat), cow)" -i SS --quiet
- @if [[ -n `diff --brief phyloFit.mod hky.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod hky.mod ; then echo "ERROR" ; exit 1 ; fi
phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat), cow)" -i SS --quiet
- @if [[ -n `diff --brief phyloFit.mod rev.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod rev.mod ; then echo "ERROR" ; exit 1 ; fi
phyloFit hmrc.ss --subst-mod UNREST --tree "(human, (mouse,rat), cow)" -i SS --quiet
- @if [[ -n `diff --brief phyloFit.mod unrest.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod unrest.mod ; then echo "ERROR" ; exit 1 ; fi
phyloFit hmrc.ss --subst-mod HKY85 --tree "(human, (mouse,rat), cow)" -i SS -k 4 --quiet
- @if [[ -n `diff --brief phyloFit.mod hky-dg.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod hky-dg.mod ; then echo "ERROR" ; exit 1 ; fi
phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat), cow)" -i SS -k 4 --quiet
- @if [[ -n `diff --brief phyloFit.mod rev-dg.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod rev-dg.mod ; then echo "ERROR" ; exit 1 ; fi
phyloFit hmrc.ss --subst-mod HKY85 --tree "(human, (mouse,rat), cow)" -i SS --EM --quiet
- @if [[ -n `diff --brief phyloFit.mod hky-em.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod hky-em.mod ; then echo "ERROR" ; exit 1 ; fi
phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat), cow)" -i SS --EM --quiet
- @if [[ -n `diff --brief phyloFit.mod rev-em.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod rev-em.mod ; then echo "ERROR" ; exit 1 ; fi
phyloFit hpmrc.ss --subst-mod REV --tree "(hg16, (mm3,rn3), galGal2)" -i SS --gaps-as-bases --quiet
- @if [[ -n `diff --brief phyloFit.mod rev-gaps.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod rev-gaps.mod ; then echo "ERROR" ; exit 1 ; fi
phyloFit hmrc.ss --subst-mod REV -i SS --init-model rev.mod --post-probs --lnl --quiet
- @if [[ -n `diff --brief phyloFit.mod rev-lnl.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
- @if [[ -n `diff --brief phyloFit.postprob rev.postprob` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod rev-lnl.mod ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.postprob rev.postprob ; then echo "ERROR" ; exit 1 ; fi
phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat))" -i SS --quiet
- @if [[ -n `diff --brief phyloFit.mod rev-hmr.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod rev-hmr.mod ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss -i SS --seqs human,mouse,rat --unordered -o SS > hmr.ss
phyloFit hmr.ss -i SS --quiet
- @if [[ -n `diff --brief phyloFit.mod rev-hmr2.mod` ]] ; then echo "ERROR" ; exit 1 ; fi # FIXME: rev-hmr.mod and rev-hmr2.mod should be equal (eq freqs being obtained from all seqs)
+ if ! diff --brief phyloFit.mod rev-hmr2.mod ; then echo "ERROR" ; exit 1 ; fi # FIXME: rev-hmr.mod and rev-hmr2.mod should be equal (eq freqs being obtained from all seqs)
msa_view hmrc.ss -i SS --seqs human,mouse --unordered -o SS > hm.ss
phyloFit hm.ss -i SS --quiet
- @if [[ -n `diff --brief phyloFit.mod rev-hm.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod rev-hm.mod ; then echo "ERROR" ; exit 1 ; fi
phyloFit hmrc.ss --subst-mod UNREST --tree "((human, mouse), cow)" -i SS --ancestor cow --quiet
- @if [[ -n `diff --brief phyloFit.mod unrest-cow-anc.mod` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief phyloFit.mod unrest-cow-anc.mod ; then echo "ERROR" ; exit 1 ; fi
@echo -e "Passed all tests.\n"
@rm -f phyloFit.mod phyloFit.postprob hmr.ss hm.ss
@@ -87,12 +87,12 @@ phyloFit:
phastCons:
@echo "*** Testing phastCons ***"
phastCons hpmrc.ss hpmrc-rev-dg-global.mod --nrates 20 --transitions .08,.008 --quiet --viterbi elements.bed --seqname chr22 > cons.dat
- @if [[ -n `diff --brief cons.dat cons_correct.dat` ]] ; then echo "ERROR" ; exit 1 ; fi
- @if [[ -n `diff --brief elements.bed elements_correct.bed` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief cons.dat cons_correct.dat ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief elements.bed elements_correct.bed ; then echo "ERROR" ; exit 1 ; fi
tree_doctor hpmrc-rev-dg-global.mod --prune galGal2 > hpmr.mod
phastCons hpmrc.ss hpmr.mod --nrates 20 --transitions .08,.008 --quiet --viterbi elements-4way.bed --seqname chr22 > cons-4way.dat
- @if [[ -n `diff --brief cons-4way.dat cons-4way_correct.dat` ]] ; then echo "ERROR" ; exit 1 ; fi
- @if [[ -n `diff --brief elements-4way.bed elements-4way_correct.bed` ]] ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief cons-4way.dat cons-4way_correct.dat ; then echo "ERROR" ; exit 1 ; fi
+ if ! diff --brief elements-4way.bed elements-4way_correct.bed ; then echo "ERROR" ; exit 1 ; fi
@echo -e "Passed all tests.\n"
@rm -f cons.dat cons-4way.dat elements.bed elements-4way.bed hpmr.mod
@@ -110,7 +110,7 @@ phyloP:
phyloP --null 10 phyloFit.mod > phyloP_null_test.txt
phyloP -i SS phyloFit.mod hmrc.ss > phyloP_sph_test.txt
phyloP -i SS --method LRT phyloFit.mod hmrc.ss > phyloP_lrt_test.txt
- phyloP -i SS --method LRT --mode CONACC phyloFit.mod hmrc.ss > phyloP_lrt_conacc_test.txt
+ phyloP -i SS --method LRT --mode CONACC phyloFit.mod hmrc.ss > phyloP_lrt_conacc_test.txt
phyloP -i SS --method GERP phyloFit.mod hmrc.ss > phyloP_gerp_test.txt
phyloP -i SS --method SCORE phyloFit.mod hmrc.ss > phyloP_score_test.txt
phyloP -i SS --method LRT --wig-scores phyloFit.mod hmrc.ss > phyloP_wig_test.wig
--- a/test/hmrc_summary_correct
+++ b/test/hmrc_summary_correct
@@ -1,5 +1,2 @@
-descrip. A C G T G+C length all_gaps some_gaps
descrip. A C G T G+C length all_gaps some_gaps
-
-hmrc.ss 0.3258 0.1913 0.1827 0.3001 0.3740 95927 0 82185
hmrc.ss 0.3258 0.1913 0.1827 0.3001 0.3740 95927 0 82185
debian/patches/series
View file @ 822eeb78
......@@ -3,3 +3,4 @@ do_not_install_to_opt.patch
use_debian_packaged_libpcre.patch
use_debian_packaged_help2man.patch
hardening.patch
fix_test_makefile.patch
debian/rules
View file @ 822eeb78
......@@ -10,3 +10,8 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
override_dh_auto_clean:
dh_auto_clean
cd src && make clean
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
cd test && PATH=$(CURDIR)/bin:$(PATH) make msa_view
endif