Mercurial > repos > saketkc > polyphen2
changeset 3:3c40b02934ad draft default tip
Uploaded
| author | saketkc |
|---|---|
| date | Tue, 07 Oct 2014 18:56:07 -0400 |
| parents | f8f4ad14f5a6 |
| children | |
| files | polyphen2_web/polyphen2_web.py polyphen2_web/polyphen2_web.xml polyphen2_web/test-data/chasm_input.txt polyphen2_web/test-data/ma_empty.csv polyphen2_web/test-data/ma_nucleotide_output.csv polyphen2_web/test-data/ma_proper_nucleotide.csv polyphen2_web/test-data/ma_proper_protein.csv polyphen2_web/test-data/ma_proper_protein.tsv polyphen2_web/test-data/ma_protein_output.csv polyphen2_web/test-data/polyphen_input.txt polyphen2_web/test-data/polyphen_output_full.tsv polyphen2_web/test-data/polyphen_output_log.tsv polyphen2_web/test-data/polyphen_output_short.tsv polyphen2_web/test-data/polyphen_output_snp.tsv polyphen2_web/tool_dependencies.xml |
| diffstat | 14 files changed, 123 insertions(+), 36 deletions(-) [+] |
line wrap: on
line diff
--- a/polyphen2_web/polyphen2_web.py Mon Apr 14 17:50:33 2014 -0400 +++ b/polyphen2_web/polyphen2_web.py Tue Oct 07 18:56:07 2014 -0400 @@ -11,10 +11,9 @@ submission_url = 'http://genetics.bwh.harvard.edu/cgi-bin/ggi/ggi2.cgi' result_url = 'http://genetics.bwh.harvard.edu' -refresh_interval = 30 -TIMEOUT = 60 * 60 -TIME_DELAY = 7 -MAX_TRIES = 30 +TIMEOUT = 60 * 60 * 24 +TIME_DELAY = 30 +MAX_TRIES = 900000000 # Genome assembly version used for chromosome # coordinates of the SNPs in user input
--- a/polyphen2_web/polyphen2_web.xml Mon Apr 14 17:50:33 2014 -0400 +++ b/polyphen2_web/polyphen2_web.xml Tue Oct 07 18:56:07 2014 -0400 @@ -55,6 +55,18 @@ <output name="short_file" file="polyphen2_short.txt"/> <output name="snp_file" file="polyphen2_snp.txt"/> </test> + <test> + <param name="input" value="polyphen_input.txt"/> + <param name="ucscdb" value="hg19"/> + <param name="model" value="HumDiv"/> + <param name="filter" value="All"/> + <param name="function" value="All"/> + <output name="log_file" file="polyphen_output_log.tsv"/> + <output name="full_file" file="polyphen_output_full.tsv"/> + <output name="short_file" file="polyphen_output_short.tsv"/> + <output name="snp_file" file="polyphen_output_snp.tsv"/> + </test> + </tests> <help> **What it does**
--- a/polyphen2_web/test-data/chasm_input.txt Mon Apr 14 17:50:33 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -TR1 chr22 30421786 + A T -TR2 chr22 29446079 + A G -TR3 chr22 29446079 + A G -TR4 chr22 40814500 - A G -TR5 chr22 40815256 + C T
--- a/polyphen2_web/test-data/ma_nucleotide_output.csv Mon Apr 14 17:50:33 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -"","Mutation","AA variant","Gene","MSA","PDB","Func. Impact","FI score","Uniprot","Refseq","MSA height","Codon start position","Func. region","Protein bind.site","DNA/RNA bind.site","small.mol bind.site" -"1","hg19,13,32912555,G,T","D1355Y","BRCA2","http://getma.org/?cm=msa&ty=f&p=BRCA2_HUMAN&rb=1247&re=1420&var=D1355Y","","low","1.24","BRCA2_HUMAN","NP_000050","14","chr13:32912555","","","","" -"2","hg19,7,55178574,G,A","","","","","","","","","0","","","","","" -"3","hg19,7,55178574,G,A","","","","","","","","","0","","","","",""
--- a/polyphen2_web/test-data/ma_proper_nucleotide.csv Mon Apr 14 17:50:33 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -13,32912555,G,T BRCA2 -7,55178574,G,A GBM -7,55178574,G,A GBM
--- a/polyphen2_web/test-data/ma_proper_protein.csv Mon Apr 14 17:50:33 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -EGFR_HUMAN,R521K -EGFR_HUMAN,R98Q,Polymorphism -EGFR_HUMAN,G719D,disease -NP_000537,G356A -NP_000537,G360A,dbSNP:rs35993958 -NP_000537,S46A,Abolishes,phosphorylation
--- a/polyphen2_web/test-data/ma_proper_protein.tsv Mon Apr 14 17:50:33 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -EGFR_HUMAN R521K -EGFR_HUMAN R98Q Polymorphism -EGFR_HUMAN G719D disease -NP_000537 G356A -NP_000537 G360A dbSNP:rs35993958 -NP_000537 S46A Abolishes phosphorylation
--- a/polyphen2_web/test-data/ma_protein_output.csv Mon Apr 14 17:50:33 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -"","Mutation","AA variant","Gene","MSA","PDB","Func. Impact","FI score","Uniprot","Refseq","MSA height","Codon start position","Func. region","Protein bind.site","DNA/RNA bind.site","small.mol bind.site" -"1","EGFR_HUMAN R521K","R521K","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=482&re=681&var=R521K","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=482&to=681&var=R521K","neutral","0.405","EGFR_HUMAN","NP_005219","399","chr7:55196748","1","1","","" -"2","EGFR_HUMAN R98Q","R98Q","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=57&re=168&var=R98Q","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=57&to=168&var=R98Q","neutral","0.6","EGFR_HUMAN","NP_005219","181","chr7:55178543","","","","" -"3","EGFR_HUMAN G719D","G719D","EGFR","http://getma.org/?cm=msa&ty=f&p=EGFR_HUMAN&rb=712&re=968&var=G719D","http://getma.org/pdb.php?prot=EGFR_HUMAN&from=712&to=968&var=G719D","medium","3.115","EGFR_HUMAN","NP_005219","700","chr7:55209201","1","1","","0UN IRE FMM ANP CY7 HYZ 03P ITI DKI 685 T95 T74 ZZY M97 6XP 0K0 KRW 0JJ 0K1 P17 112 1N1 JIN STI P5C 585 S19 P16 VX6 P3Y SX7 ACK B90 AMP ZD6 STU 7PY BI9 BII ATP ADP 4ST VG8 YAM P1E 7X4 7X5 7X6 7X8 349 3JZ" -"4","NP_000537 G356A","G356A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=318&re=359&var=G356A","http://getma.org/pdb.php?prot=P53_HUMAN&from=318&to=359&var=G356A","neutral","-0.895","P53_HUMAN","NP_000537","45","chr17:7514684","","1","","" -"5","NP_000537 G360A","G360A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=360&re=393&var=G360A","","medium","2.25","P53_HUMAN","NP_000537","15","chr17:7514672","","","","" -"6","NP_000537 S46A","S46A","TP53","http://getma.org/?cm=msa&ty=f&p=P53_HUMAN&rb=30&re=94&var=S46A","http://getma.org/pdb.php?prot=P53_HUMAN&from=30&to=94&var=S46A","neutral","0.55","P53_HUMAN","NP_000537","5","chr17:7520274","1","1","",""
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/polyphen_input.txt Tue Oct 07 18:56:07 2014 -0400 @@ -0,0 +1,7 @@ +Q92889 706 I T +Q92889 875 E G +XRCC1_HUMAN 399 R Q +NP_005792 59 L P +rs1799931 +chr1:1267483 G/A +chr1:1158631 A/C,G,T
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/polyphen_output_full.tsv Tue Oct 07 18:56:07 2014 -0400 @@ -0,0 +1,20 @@ +#o_acc o_pos o_aa1 o_aa2 rsid acc pos aa1 aa2 nt1 nt2 prediction based_on effect pph2_class pph2_prob pph2_FPR pph2_TPR pph2_FDR site region PHAT dScore Score1 Score2 MSAv Nobs Nstruct Nfilt PDB_id PDB_pos PDB_ch ident length NormASA SecStr MapReg dVol dProp B-fact H-bonds AveNHet MinDHet AveNInt MinDInt AveNSit MinDSit Transv CodPos CpG MinDJxn PfamHit IdPmax IdPSNP IdQmin +Q92889 706 I T rs1800069 Q92889 706 I T T C probably damaging alignment ? deleterious 1 0.00026 0.00018 0.0109 NO NO ? +2.055 -1.216 -3.271 2 52 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 1 0 -100 PF02732.10 0.730 ? 14.63 +Q92889 875 E G rs1800124 Q92889 875 E G A G possibly damaging alignment ? deleterious 0.937 0.0566 0.801 0.0874 NO NO ? +1.645 -1.600 -3.245 2 51 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 1 0 -607 NO 3.009 ? 63.97 +XRCC1_HUMAN 399 R Q rs25487 P18887 399 R Q G A probably damaging alignment ? deleterious 0.979 0.0411 0.755 0.0687 NO NO ? +1.579 -1.999 -3.578 2 86 20 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 1 1 +4 NO 2.498 ? 46.92 +NP_005792 59 L P rs3390 P41567 59 L P T C possibly damaging structure 1.1.1 deleterious 0.895 0.0631 0.82 0.0945 NO NO ? +1.235 -1.254 -2.489 2 104 4 1 2if1 72 A 1.00 113 0.007 H A -55 1.07 0.00 ? ? ? ? ? ? ? 0 1 0 +20 PF01253.17 45.533 45.533 92.04 +rs1799931 ? ? ? rs1799931 P11245 286 G E G A benign alignment ? neutral 0.317 0.112 0.903 0.144 NO NO ? +1.145 -2.309 -3.454 2 59 20 2 2pfr 286 A 1.00 289 0.172 S l 78 0.75 -0.03 ? ? ? ? ? ? ? 0 1 0 -863 NO 8.156 ? 82.41 +Q7RTX0 191 R H ? Q7RTX0 191 R H G A probably damaging alignment ? deleterious 0.998 0.0112 0.273 0.0274 NO NO ? +2.547 -1.839 -4.386 2 57 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 1 1 -164 PF01094.23 2.232 ? 72.89 # chr1:1267483|GA|uc010nyk.1+|TAS1R3|NP_689414 +Q9BRK5 190 D E ? Q9BRK5 190 D E T G possibly damaging alignment ? neutral 0.454 0.0996 0.889 0.132 NO NO ? +0.793 -1.779 -2.572 2 87 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 2 0 +8 NO 7.550 7.550 41.99 # chr1:1158631|AC|uc001adh.3-|SDF4|NP_057260 +Q9BRK5 190 D E ? Q9BRK5 190 D E T A possibly damaging alignment ? neutral 0.454 0.0996 0.889 0.132 NO NO ? +0.793 -1.779 -2.572 2 87 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 2 0 +8 NO 7.550 7.550 41.99 # chr1:1158631|AT|uc001adh.3-|SDF4|NP_057260 +Q9BRK5-6 190 D E ? Q9BRK5-6 190 D E T G probably damaging alignment ? deleterious 0.998 0.0112 0.273 0.0274 ? ? ? +1.566 -1.300 -2.866 2 46 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 2 0 +8 ? 2.573 ? 36.21 # chr1:1158631|AC|uc001adi.3-|SDF4|NP_057631 +Q9BRK5-6 190 D E ? Q9BRK5-6 190 D E T A probably damaging alignment ? deleterious 0.998 0.0112 0.273 0.0274 ? ? ? +1.566 -1.300 -2.866 2 46 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 2 0 +8 ? 2.573 ? 36.21 # chr1:1158631|AT|uc001adi.3-|SDF4|NP_057631 +Q9BRK5 190 D E ? Q9BRK5 190 D E T G possibly damaging alignment ? neutral 0.454 0.0996 0.889 0.132 NO NO ? +0.793 -1.779 -2.572 2 87 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 2 0 -580 NO 7.550 7.550 41.99 # chr1:1158631|AC|uc001adj.1-|SDF4| +Q9BRK5 190 D E ? Q9BRK5 190 D E T A possibly damaging alignment ? neutral 0.454 0.0996 0.889 0.132 NO NO ? +0.793 -1.779 -2.572 2 87 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 2 0 -580 NO 7.550 7.550 41.99 # chr1:1158631|AT|uc001adj.1-|SDF4| +Q9BRK5 190 D E ? Q9BRK5 190 D E T G possibly damaging alignment ? neutral 0.454 0.0996 0.889 0.132 NO NO ? +0.793 -1.779 -2.572 2 87 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 2 0 +8 NO 7.550 7.550 41.99 # chr1:1158631|AC|uc009vjv.2-|SDF4|NP_057260 +Q9BRK5 190 D E ? Q9BRK5 190 D E T A possibly damaging alignment ? neutral 0.454 0.0996 0.889 0.132 NO NO ? +0.793 -1.779 -2.572 2 87 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 1 2 0 +8 NO 7.550 7.550 41.99 # chr1:1158631|AT|uc009vjv.2-|SDF4|NP_057260 +## Sources: +## Predictions: PolyPhen-2 v2.2.2r398 +## Sequences: UniProtKB/UniRef100 Release 2011_12 (14-Dec-2011) +## Structures: PDB/DSSP Snapshot 03-Jan-2012 (78304 Structures) +## Genes: UCSC MultiZ46Way GRCh37/hg19 (08-Oct-2009)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/polyphen_output_log.tsv Tue Oct 07 18:56:07 2014 -0400 @@ -0,0 +1,36 @@ +=========================== +Stage 1/7: Validating input +=========================== +No errors + +=============================== +Stage 2/7: Mapping genomic SNPs +=============================== +No errors + +============================ +Stage 3/7: Collecting output +============================ +No errors + +=============================================== +Stage 4/7: Building MSA and annotating proteins +=============================================== +(XRCC1_HUMAN:399:R/Q) WARNING: find_gene: Swapped codons (CAG>CGG) in uc002owt.2 nucleotide sequence at position: 1195 +(XRCC1_HUMAN:399:R/Q) WARNING: Replaced reference AA residue (Q) with (R) in uc002owt.2 protein sequence at position: 399 +Total errors/warnings: 2 + +============================ +Stage 5/7: Collecting output +============================ +No errors + +===================== +Stage 6/7: Predicting +===================== +No errors + +============================= +Stage 7/7: Generating reports +============================= +No errors
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/polyphen_output_short.tsv Tue Oct 07 18:56:07 2014 -0400 @@ -0,0 +1,20 @@ +#o_acc o_pos o_aa1 o_aa2 rsid acc pos aa1 aa2 prediction pph2_prob pph2_FPR pph2_TPR +Q92889 706 I T rs1800069 Q92889 706 I T probably damaging 1 0.00026 0.00018 +Q92889 875 E G rs1800124 Q92889 875 E G possibly damaging 0.937 0.0566 0.801 +XRCC1_HUMAN 399 R Q rs25487 P18887 399 R Q probably damaging 0.979 0.0411 0.755 +NP_005792 59 L P rs3390 P41567 59 L P possibly damaging 0.895 0.0631 0.82 +rs1799931 ? ? ? rs1799931 P11245 286 G E benign 0.317 0.112 0.903 +Q7RTX0 191 R H ? Q7RTX0 191 R H probably damaging 0.998 0.0112 0.273 # chr1:1267483|GA|uc010nyk.1+|TAS1R3|NP_689414 +Q9BRK5 190 D E ? Q9BRK5 190 D E possibly damaging 0.454 0.0996 0.889 # chr1:1158631|AC|uc001adh.3-|SDF4|NP_057260 +Q9BRK5 190 D E ? Q9BRK5 190 D E possibly damaging 0.454 0.0996 0.889 # chr1:1158631|AT|uc001adh.3-|SDF4|NP_057260 +Q9BRK5-6 190 D E ? Q9BRK5-6 190 D E probably damaging 0.998 0.0112 0.273 # chr1:1158631|AC|uc001adi.3-|SDF4|NP_057631 +Q9BRK5-6 190 D E ? Q9BRK5-6 190 D E probably damaging 0.998 0.0112 0.273 # chr1:1158631|AT|uc001adi.3-|SDF4|NP_057631 +Q9BRK5 190 D E ? Q9BRK5 190 D E possibly damaging 0.454 0.0996 0.889 # chr1:1158631|AC|uc001adj.1-|SDF4| +Q9BRK5 190 D E ? Q9BRK5 190 D E possibly damaging 0.454 0.0996 0.889 # chr1:1158631|AT|uc001adj.1-|SDF4| +Q9BRK5 190 D E ? Q9BRK5 190 D E possibly damaging 0.454 0.0996 0.889 # chr1:1158631|AC|uc009vjv.2-|SDF4|NP_057260 +Q9BRK5 190 D E ? Q9BRK5 190 D E possibly damaging 0.454 0.0996 0.889 # chr1:1158631|AT|uc009vjv.2-|SDF4|NP_057260 +## Sources: +## Predictions: PolyPhen-2 v2.2.2r398 +## Sequences: UniProtKB/UniRef100 Release 2011_12 (14-Dec-2011) +## Structures: PDB/DSSP Snapshot 03-Jan-2012 (78304 Structures) +## Genes: UCSC MultiZ46Way GRCh37/hg19 (08-Oct-2009)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/polyphen2_web/test-data/polyphen_output_snp.tsv Tue Oct 07 18:56:07 2014 -0400 @@ -0,0 +1,24 @@ +#snp_pos str gene transcript ccid ccds cciden refa type ntpos nt1 nt2 flanks trv cpg jxdon jxacc exon cexon jxc dgn cdnpos frame cdn1 cdn2 aa1 aa2 aapos spmap spacc spname refs_acc dbrsid dbobsrvd dbavHet dbavHetSE dbRmPaPt comments +chr1:1267483 + TAS1R3 uc010nyk.1 59 CCDS30556.1 0.999 G/A missense 758 G A CT 0 1 -164 -80 3/6 3/6 ? 0 191 1 CGT CAT R H 191 1 Q7RTX0 TS1R3_HUMAN NP_689414 rs141717515 A/G 0.00063 0.017742 G>G>G +chr1:1158631 - SDF4 uc001adh.3 49 CCDS30553.1 1 A/C missense 8817 T G AG 1 0 +8 -107 4/7 3/6 ? 2 190 2 GAT GAG D E 190 1 Q9BRK5 CAB45_HUMAN NP_057260 ? ? ? ? ? +chr1:1158631 - SDF4 uc001adh.3 49 CCDS30553.1 1 A/G coding-synon 8817 T C AG 0 2 +8 -107 4/7 3/6 ? 2 190 2 GAT GAC D D 190 1 Q9BRK5 CAB45_HUMAN NP_057260 rs6603781 T/C 0.133948 0.221431 T>C>C +chr1:1158631 - SDF4 uc001adh.3 49 CCDS30553.1 1 A/T missense 8817 T A AG 1 0 +8 -107 4/7 3/6 ? 2 190 2 GAT GAA D E 190 1 Q9BRK5 CAB45_HUMAN NP_057260 ? ? ? ? ? +chr1:1158631 - SDF4 uc001adi.3 ? CCDS12.1 1 A/C missense 8817 T G AG 1 0 +8 -107 4/7 3/6 ? 2 190 2 GAT GAG D E 190 1 Q9BRK5-6 CAB45_HUMAN NP_057631 ? ? ? ? ? +chr1:1158631 - SDF4 uc001adi.3 ? CCDS12.1 1 A/G coding-synon 8817 T C AG 0 2 +8 -107 4/7 3/6 ? 2 190 2 GAT GAC D D 190 1 Q9BRK5-6 CAB45_HUMAN NP_057631 rs6603781 T/C 0.133948 0.221431 T>C>C +chr1:1158631 - SDF4 uc001adi.3 ? CCDS12.1 1 A/T missense 8817 T A AG 1 0 +8 -107 4/7 3/6 ? 2 190 2 GAT GAA D E 190 1 Q9BRK5-6 CAB45_HUMAN NP_057631 ? ? ? ? ? +chr1:1158631 - SDF4 uc001adj.1 ? ? ? A/C missense 718 T G AG 1 0 -580 -107 2/2 2/2 ? 2 68 2 GAT GAG D E 190 1 Q9BRK5 CAB45_HUMAN ? ? ? ? ? ? +chr1:1158631 - SDF4 uc001adj.1 ? ? ? A/G coding-synon 718 T C AG 0 2 -580 -107 2/2 2/2 ? 2 68 2 GAT GAC D D 190 1 Q9BRK5 CAB45_HUMAN ? rs6603781 T/C 0.133948 0.221431 T>C>C +chr1:1158631 - SDF4 uc001adj.1 ? ? ? A/T missense 718 T A AG 1 0 -580 -107 2/2 2/2 ? 2 68 2 GAT GAA D E 190 1 Q9BRK5 CAB45_HUMAN ? ? ? ? ? ? +chr1:1158631 - SDF4 uc009vjv.2 ? ? ? A/C missense 8817 T G AG 1 0 +8 -107 3/6 2/5 ? 2 68 2 GAT GAG D E 190 1 Q9BRK5 CAB45_HUMAN NP_057260 ? ? ? ? ? +chr1:1158631 - SDF4 uc009vjv.2 ? ? ? A/G coding-synon 8817 T C AG 0 2 +8 -107 3/6 2/5 ? 2 68 2 GAT GAC D D 190 1 Q9BRK5 CAB45_HUMAN NP_057260 rs6603781 T/C 0.133948 0.221431 T>C>C +chr1:1158631 - SDF4 uc009vjv.2 ? ? ? A/T missense 8817 T A AG 1 0 +8 -107 3/6 2/5 ? 2 68 2 GAT GAA D E 190 1 Q9BRK5 CAB45_HUMAN NP_057260 ? ? ? ? ? +## Totals: +## lines input 2 +## lines skipped 0 +## alleles annotated 13 +## missense 9 +## nonsense 0 +## coding-synon 4 +## intron 0 +## utr-3 0 +## utr-5 0
--- a/polyphen2_web/tool_dependencies.xml Mon Apr 14 17:50:33 2014 -0400 +++ b/polyphen2_web/tool_dependencies.xml Tue Oct 07 18:56:07 2014 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="beautifulsoup4" version="4.1.0"> - <repository changeset_revision="829eeedb1083" name="package_beautifulsoup4_4_1_0" owner="saketkc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="df0beb7ea718" name="package_beautifulsoup4_4_1_0" owner="saketkc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>