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 <[email protected]> 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 <[email protected]> -remove sprot.seq relative tests (and data) due to not compatible license +Debian packaging patch, 21/03/2011 Olivier Sallou <[email protected]> +--- 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
