[med-svn] r6357 - in trunk/packages/squizz/trunk/debian: . patches
olivier sallou
osallou-guest at alioth.debian.org
Mon Mar 21 14:33:42 UTC 2011
Author: osallou-guest
Date: 2011-03-21 14:33:35 +0000 (Mon, 21 Mar 2011)
New Revision: 6357
Added:
trunk/packages/squizz/trunk/debian/README.source
trunk/packages/squizz/trunk/debian/get-orig-source
Modified:
trunk/packages/squizz/trunk/debian/patches/debianpackaging
trunk/packages/squizz/trunk/debian/rules
trunk/packages/squizz/trunk/debian/watch
Log:
remove licensed file from source with a get-orig-source
Added: trunk/packages/squizz/trunk/debian/README.source
===================================================================
--- trunk/packages/squizz/trunk/debian/README.source (rev 0)
+++ trunk/packages/squizz/trunk/debian/README.source 2011-03-21 14:33:35 UTC (rev 6357)
@@ -0,0 +1,3 @@
+Default source includes a test data file with incompatible license. To woraround this, one should use the get-orig-source command to update the source which will remove the involved file. A patch is also required to remove from build step the tests using this data file.
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Mon, 21 Mar 2011 15:32:00 +0100
Added: trunk/packages/squizz/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/squizz/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/squizz/trunk/debian/get-orig-source 2011-03-21 14:33:35 UTC (rev 6357)
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+set -e
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --verbose --force-download | \
+ grep "Newest version on remote site is .* local version is .*" | \
+ head -n 1 | \
+ sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
+
+mkdir -p ../tarballs
+cd ../tarballs
+
+UTAR="${PKG}_${VERSION}.orig.tar.gz"
+mv ../${UTAR} .
+tar -xzf ${UTAR}
+
+cd $PKG-${VERSION}
+rm -f test/sequence/sprot.seq
+cd ..
+
+rm $UTAR
+
+GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "${PKG}-${VERSION}"
+rm -rf "${PKG}-${VERSION}"
+
Modified: trunk/packages/squizz/trunk/debian/patches/debianpackaging
===================================================================
--- trunk/packages/squizz/trunk/debian/patches/debianpackaging 2011-03-21 13:23:31 UTC (rev 6356)
+++ trunk/packages/squizz/trunk/debian/patches/debianpackaging 2011-03-21 14:33:35 UTC (rev 6357)
@@ -1,5 +1,30 @@
-Patch for Debian packaging - 21/03/2011 Olivier Sallou <olivier.sallou at irisa.fr>
-remove sprot.seq relative tests (and data) due to not compatible license
+Debian packaging patch, 21/03/2011 Olivier Sallou <olivier.sallou at irisa.fr>
+--- a/doc/alifmt.man
++++ b/doc/alifmt.man
+@@ -128,8 +128,8 @@
+ .rm #[ #] #H #V #F C
+ .\" ========================================================================
+ .\"
+-.IX Title "ALIFMT 1"
+-.TH ALIFMT 1 "2009-05-19" "Unix" "User Manuals"
++.IX Title "ALIFMT 5"
++.TH ALIFMT 5 "2009-05-19" "Unix" "User Manuals"
+ .SH "NAME"
+ .IP "\fBalifmt\fR \- Aligned sequences formats" 4
+ .IX Item "alifmt - Aligned sequences formats"
+--- a/doc/seqfmt.man
++++ b/doc/seqfmt.man
+@@ -128,8 +128,8 @@
+ .rm #[ #] #H #V #F C
+ .\" ========================================================================
+ .\"
+-.IX Title "SEQFMT 1"
+-.TH SEQFMT 1 "2009-05-19" "Unix" "User Manuals"
++.IX Title "SEQFMT 5"
++.TH SEQFMT 5 "2009-05-19" "Unix" "User Manuals"
+ .SH "NAME"
+ .IP "\fBseqfmt\fR \- Sequences formats" 4
+ .IX Item "seqfmt - Sequences formats"
--- a/test/Makefile.am
+++ b/test/Makefile.am
@@ -4,7 +4,7 @@
@@ -50,55 +75,6 @@
## Checks EMBL-like sequence
for f in $seqlist; do
---- a/test/sprot.sh
-+++ /dev/null
-@@ -1,20 +0,0 @@
--#! /bin/sh
--
--## Verbose mode
--test "x$VERBOSE" = xx && set -x
--
--## Inits
--sequence=$srcdir/sequence/sprot.seq
--
--## Check default SWISSPROT file reference
--(../src/squizz -S -f swissprot $sequence 2>&1 | grep -v SWISSPROT) && exit 1
--
--## Check cross-reference data with internal `;'
--sed 's,Rattus norvegicus,Rattus;norvegicus,' $sequence >_tmpseq.seq
--(../src/squizz -S -f swissprot _tmpseq.seq 2>&1 | grep -v SWISSPROT) && exit 1
--
--## Cleanup
--rm -f _tmpseq.seq
--
--exit 0
--
---- a/doc/alifmt.man
-+++ b/doc/alifmt.man
-@@ -128,8 +128,8 @@
- .rm #[ #] #H #V #F C
- .\" ========================================================================
- .\"
--.IX Title "ALIFMT 1"
--.TH ALIFMT 1 "2009-05-19" "Unix" "User Manuals"
-+.IX Title "ALIFMT 5"
-+.TH ALIFMT 5 "2009-05-19" "Unix" "User Manuals"
- .SH "NAME"
- .IP "\fBalifmt\fR \- Aligned sequences formats" 4
- .IX Item "alifmt - Aligned sequences formats"
---- a/doc/seqfmt.man
-+++ b/doc/seqfmt.man
-@@ -128,8 +128,8 @@
- .rm #[ #] #H #V #F C
- .\" ========================================================================
- .\"
--.IX Title "SEQFMT 1"
--.TH SEQFMT 1 "2009-05-19" "Unix" "User Manuals"
-+.IX Title "SEQFMT 5"
-+.TH SEQFMT 5 "2009-05-19" "Unix" "User Manuals"
- .SH "NAME"
- .IP "\fBseqfmt\fR \- Sequences formats" 4
- .IX Item "seqfmt - Sequences formats"
--- a/test/fmtseq.sh
+++ b/test/fmtseq.sh
@@ -60,11 +60,6 @@
@@ -113,137 +89,3 @@
exit 0
---- a/test/sequence/sprot.seq
-+++ /dev/null
-@@ -1,131 +0,0 @@
--ID UBR5_RAT Reviewed; 920 AA.
--AC Q62671;
--DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
--DT 05-MAR-2002, sequence version 2.
--DT 22-JUL-2008, entry version 60.
--DE RecName: Full=E3 ubiquitin-protein ligase UBR5;
--DE EC=6.3.2.-;
--DE AltName: Full=E3 ubiquitin-protein ligase, HECT domain-containing 1;
--DE AltName: Full=Hyperplastic discs protein homolog;
--DE AltName: Full=100 kDa protein;
--DE Flags: Fragment;
--GN Name=Ubr5; Synonyms=Dd5, Edd, Edd1, Hyd;
--OS Rattus norvegicus (Rat).
--OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
--OC Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi;
--OC Muroidea; Muridae; Murinae; Rattus.
--OX NCBI_TaxID=10116;
--RN [1]
--RP NUCLEOTIDE SEQUENCE [MRNA].
--RC STRAIN=Wistar; TISSUE=Testis;
--RX MEDLINE=92253337; PubMed=1533713; DOI=10.1093/nar/20.7.1471;
--RA Mueller D., Rehbein M., Baumeister H., Richter D.;
--RT "Molecular characterization of a novel rat protein structurally
--RT related to poly(A) binding proteins and the 70K protein of the U1
--RT small nuclear ribonucleoprotein particle (snRNP).";
--RL Nucleic Acids Res. 20:1471-1475(1992).
--RN [2]
--RP ERRATUM.
--RA Mueller D., Rehbein M., Baumeister H., Richter D.;
--RL Nucleic Acids Res. 20:2624-2624(1992).
--RN [3]
--RP IDENTIFICATION OF PROBABLE FRAMESHIFT.
--RX MEDLINE=99153743; PubMed=10030672; DOI=10.1038/sj.onc.1202249;
--RA Callaghan M.J., Russell A.J., Woollatt E., Sutherland G.R.,
--RA Sutherland R.L., Watts C.K.W.;
--RT "Identification of a human HECT family protein with homology to the
--RT Drosophila tumor suppressor gene hyperplastic discs.";
--RL Oncogene 17:3479-3491(1998).
--RN [4]
--RP TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
--RX PubMed=12239083; DOI=10.1210/en.2002-220262;
--RA Oughtred R., Bedard N., Adegoke O.A.J., Morales C.R., Trasler J.,
--RA Rajapurohitam V., Wing S.S.;
--RT "Characterization of rat100, a 300-kilodalton ubiquitin-protein ligase
--RT induced in germ cells of the rat testis and similar to the Drosophila
--RT hyperplastic discs gene.";
--RL Endocrinology 143:3740-3747(2002).
--CC -!- FUNCTION: E3 ubiquitin-protein ligase which is a component of the
--CC N-end rule pathway. Recognizes and binds to proteins bearing
--CC specific amino-terminal residues that are destabilizing according
--CC to the N-end rule, leading to their ubiquitination and subsequent
--CC degradation (By similarity). May be involved in maturation and/or
--CC post-transcriptional regulation of mRNA. May play a role in
--CC control of cell cycle progression. May have tumor suppressor
--CC function. Regulates DNA topoisomerase II binding protein (TopBP1)
--CC for the DNA damage response. Plays an essential role in
--CC extraembryonic development (By similarity).
--CC -!- PATHWAY: Protein modification; protein ubiquitination.
--CC -!- SUBUNIT: Binds TOPBP1 (By similarity).
--CC -!- SUBCELLULAR LOCATION: Nucleus (By similarity).
--CC -!- TISSUE SPECIFICITY: Highest levels found in testis. Also present
--CC in liver, kidney, lung and brain.
--CC -!- DEVELOPMENTAL STAGE: In early postnatal life, expression in the
--CC testis increases to reach a maximum around day 28.
--CC -!- PTM: Phosphorylated upon DNA damage, probably by ATM or ATR (By
--CC similarity).
--CC -!- MISCELLANEOUS: A cysteine residue is required for ubiquitin-
--CC thioester formation.
--CC -!- SIMILARITY: Contains 1 HECT (E6AP-type E3 ubiquitin-protein
--CC ligase) domain.
--CC -!- SIMILARITY: Contains 1 PABC domain.
--CC -!- SEQUENCE CAUTION:
--CC Sequence=CAA45756.1; Type=Frameshift; Positions=30;
--CC -----------------------------------------------------------------------
--CC Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
--CC Distributed under the Creative Commons Attribution-NoDerivs License
--CC -----------------------------------------------------------------------
--DR EMBL; X64411; CAA45756.1; ALT_FRAME; mRNA.
--DR PIR; S22659; S22659.
--DR UniGene; Rn.54812; -.
--DR HSSP; O95071; 1I2T.
--DR SMR; Q62671; 515-575.
--DR PhosphoSite; Q62671; -.
--DR Ensembl; ENSRNOG00000006816; Rattus norvegicus.
--DR RGD; 621236; Dd5.
--DR HOVERGEN; Q62671; -.
--DR ArrayExpress; Q62671; -.
--DR GermOnline; ENSRNOG00000006816; Rattus norvegicus.
--DR InterPro; IPR000569; HECT.
--DR InterPro; IPR002004; PABP_HYD.
--DR Gene3D; G3DSA:1.10.1900.10; PABP_HYD; 1.
--DR Pfam; PF00632; HECT; 1.
--DR Pfam; PF00658; PABP; 1.
--DR SMART; SM00119; HECTc; 1.
--DR SMART; SM00517; PolyA; 1.
--DR PROSITE; PS50237; HECT; 1.
--DR PROSITE; PS51309; PABC; 1.
--PE 2: Evidence at transcript level;
--KW Ligase; Nucleus; Phosphoprotein; Ubl conjugation pathway.
--FT CHAIN <1 920 E3 ubiquitin-protein ligase UBR5.
--FT /FTId=PRO_0000086933.
--FT DOMAIN 499 576 PABC.
--FT DOMAIN 583 920 HECT.
--FT COMPBIAS 108 119 Asp/Glu-rich (acidic).
--FT COMPBIAS 158 181 Pro-rich.
--FT COMPBIAS 451 470 Arg/Glu-rich (mixed charge).
--FT COMPBIAS 479 488 Arg/Asp-rich (mixed charge).
--FT COMPBIAS 610 621 Asp/Glu-rich (acidic).
--FT COMPBIAS 858 878 Pro-rich.
--FT ACT_SITE 889 889 Glycyl thioester intermediate (By
--FT similarity).
--FT MOD_RES 193 193 Phosphoserine (By similarity).
--FT NON_TER 1 1
--SQ SEQUENCE 920 AA; 103950 MW; 465771084536C3AA CRC64;
-- ARRERMTARE EASLRTLEGR RRATLLSARQ GMMSARGDFL NYALSLMRSH NDEHSDVLPV
-- LDVCSLKHVA YVFQALIYWI KAMNQQTTLD TPQLERKRTR ELLELGIDNE DSEHENDDDT
-- SQSATLNDKD DESLPAETGQ NHPFFRRSDS MTFLGCIPPN PFEVPLAEAI PLADQPHLLQ
-- PNARKEDLFG RPSQGLYSSS AGSGKCLVEV TMDRNCLEVL PTKMSYAANL KNVMNMQNRQ
-- KKAGEDQSML AEEADSSKPG PSAHDVAAQL KSSLLAEIGL TESEGPPLTS FRPQCSFMGM
-- VISHDMLLGR WRLSLELFGR VFMEDVGAEP GSILTELGGF EVKESKFRRE MEKLRNQQSR
-- DLSLEVDRDR DLLIQQTMRQ LNNHFGRRCA TTPMAVHRVK VTFKDEPGEG SGVARSFYTA
-- IAQAFLSNEK LPNLDCIQNA NKGTHTSLMQ RLRNRGERDR EREREREMRR SSGLRAGSRR
-- DRDRDFRRQL SIDTRPFRPA SEGNPSDDPD PLPAHRQALG ERLYPRVQAM QPAFASKITG
-- MLLELSPAQL LLLLASEDSL RARVEEAMEL IVAHGRENGA DSILDLGLLD SSEKVQENRK
-- RHGSSRSVVD MDLDDTDDGD DNAPLFYQPG KRGFYTPRPG KNTEARLNCF RNIGRILGLC
-- LLQNELCPIT LNRHVIKVLL GRKVNWHDFA FFDPVMYESL RQLILASQSS DADAVFSAMD
-- LAFAVDLCKE EGGGQVELIP NGVNIPVTPQ NVYEYVRKYA EHRMLVVAEQ PLHAMRKGLL
-- DVLPKNSLED LTAEDFRLLV NGCGEVNVQM LISFTSFNDE SGENAEKLLQ FKRWFWSIVE
-- RMSMTERQDL VYFWTSSPSL PASEEGFQPM PSITIRPPDD QHLPTANTCI SRLYVPLYSS
-- KQILKQKLLL AIKTKNFGFV
--//
Modified: trunk/packages/squizz/trunk/debian/rules
===================================================================
--- trunk/packages/squizz/trunk/debian/rules 2011-03-21 13:23:31 UTC (rev 6356)
+++ trunk/packages/squizz/trunk/debian/rules 2011-03-21 14:33:35 UTC (rev 6357)
@@ -6,3 +6,6 @@
%:
dh $@
+
+get-orig-source:
+ . debian/get-orig-source
Modified: trunk/packages/squizz/trunk/debian/watch
===================================================================
--- trunk/packages/squizz/trunk/debian/watch 2011-03-21 13:23:31 UTC (rev 6356)
+++ trunk/packages/squizz/trunk/debian/watch 2011-03-21 14:33:35 UTC (rev 6357)
@@ -3,5 +3,5 @@
# Uncommment to examine a FTP server
#ftp://ftp.example.com/pub/squizz-(.*)\.tar\.gz debian uupdate
-opts=passive,filenamemangle=s/_/./g;s/tar\.gz/orig\.tar\.gz/g ftp://ftp.pasteur.fr/pub/gensoft/projects/squizz/squizz-(.*)\.tar\.gz debian uupdate
+opts=passive,filenamemangle=s/_/./g;s/-/_/g;s/tar\.gz/orig\.tar\.gz/g ftp://ftp.pasteur.fr/pub/gensoft/projects/squizz/squizz-(.*)\.tar\.gz debian uupdate
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