[med-svn] r6336 - in trunk/packages/squizz/trunk/debian: . patches
olivier sallou
osallou-guest at alioth.debian.org
Mon Mar 21 09:26:21 UTC 2011
Author: osallou-guest
Date: 2011-03-21 09:26:17 +0000 (Mon, 21 Mar 2011)
New Revision: 6336
Added:
trunk/packages/squizz/trunk/debian/patches/
trunk/packages/squizz/trunk/debian/patches/debianpackaging
trunk/packages/squizz/trunk/debian/patches/series
Modified:
trunk/packages/squizz/trunk/debian/squizz.manpages
Log:
patch man pages and remove test incompatblie license file and tests
Added: trunk/packages/squizz/trunk/debian/patches/debianpackaging
===================================================================
--- trunk/packages/squizz/trunk/debian/patches/debianpackaging (rev 0)
+++ trunk/packages/squizz/trunk/debian/patches/debianpackaging 2011-03-21 09:26:17 UTC (rev 6336)
@@ -0,0 +1,249 @@
+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
+--- a/test/Makefile.am
++++ b/test/Makefile.am
+@@ -4,7 +4,7 @@
+
+ TESTS_ALIS = clustal.sh mega.sh msf.sh nexus.sh phylipi.sh phylips.sh \
+ stockholm.sh
+-TESTS_SEQS = embl.sh genbank.sh ig.sh raw.sh sprot.sh
++TESTS_SEQS = embl.sh genbank.sh ig.sh raw.sh
+
+ XFAIL_TESTS =
+
+@@ -16,6 +16,6 @@
+ SEQS = sequence/embl.seq sequence/fasta.seq sequence/gde.seq \
+ sequence/genbank.seq sequence/genpept.seq sequence/gcg.seq \
+ sequence/ig.seq sequence/nbrf.seq sequence/pir.seq sequence/raw.seq \
+- sequence/refseqn.seq sequence/refseqp.seq sequence/sprot.seq
++ sequence/refseqn.seq sequence/refseqp.seq
+
+ EXTRA_DIST = $(TESTS) $(DATAS)
+--- a/test/Makefile.in
++++ b/test/Makefile.in
+@@ -178,7 +178,7 @@
+ TESTS_ALIS = clustal.sh mega.sh msf.sh nexus.sh phylipi.sh phylips.sh \
+ stockholm.sh
+
+-TESTS_SEQS = embl.sh genbank.sh ig.sh raw.sh sprot.sh
++TESTS_SEQS = embl.sh genbank.sh ig.sh raw.sh
+ DATAS = $(ALIS) $(SEQS)
+ ALIS = align/clustal.seq align/fasta.seq align/mega.seq align/msf.seq \
+ align/nexusi.seq align/phylipi.seq align/phylips.seq align/stock.seq
+@@ -186,7 +186,7 @@
+ SEQS = sequence/embl.seq sequence/fasta.seq sequence/gde.seq \
+ sequence/genbank.seq sequence/genpept.seq sequence/gcg.seq \
+ sequence/ig.seq sequence/nbrf.seq sequence/pir.seq sequence/raw.seq \
+- sequence/refseqn.seq sequence/refseqp.seq sequence/sprot.seq
++ sequence/refseqn.seq sequence/refseqp.seq
+
+ EXTRA_DIST = $(TESTS) $(DATAS)
+ all: all-am
+--- a/test/convseq.sh
++++ b/test/convseq.sh
+@@ -7,7 +7,7 @@
+
+ ## Sequence files location
+ seqdir=$srcdir/sequence
+-seqlist='embl.seq fasta.seq gcg.seq gde.seq genbank.seq genpept.seq ig.seq nbrf.seq pir.seq raw.seq refseqn.seq refseqp.seq sprot.seq'
++seqlist='embl.seq fasta.seq gcg.seq gde.seq genbank.seq genpept.seq ig.seq nbrf.seq pir.seq raw.seq refseqn.seq refseqp.seq'
+
+ ## 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 @@
+ (../src/squizz $srcdir/$f 2>&1 | grep -v RAW) && exit 1
+ done
+
+-## Checks SWISSPROT-like sequence
+-seqlist='sprot.seq'
+-for f in $seqlist; do
+- (../src/squizz $srcdir/$f 2>&1 | grep -v SWISSPROT) && exit 1
+-done
+
+ 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
+-//
Added: trunk/packages/squizz/trunk/debian/patches/series
===================================================================
--- trunk/packages/squizz/trunk/debian/patches/series (rev 0)
+++ trunk/packages/squizz/trunk/debian/patches/series 2011-03-21 09:26:17 UTC (rev 6336)
@@ -0,0 +1 @@
+debianpackaging
Modified: trunk/packages/squizz/trunk/debian/squizz.manpages
===================================================================
--- trunk/packages/squizz/trunk/debian/squizz.manpages 2011-03-21 09:22:02 UTC (rev 6335)
+++ trunk/packages/squizz/trunk/debian/squizz.manpages 2011-03-21 09:26:17 UTC (rev 6336)
@@ -1 +1 @@
-debian/squizz.1
+doc/squizz.man
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