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--- setupguide:seqrepoinstall [2016/02/04 10:12]
132.168.72.225 créée
+++ setupguide:seqrepoinstall [2016/07/07 14:11] (current)
132.168.72.225 [Running Sequence Repository]
@@ Line 103: / Line 103: @@
-** Testing rules **
+===== Testing rules  =====
-In order to verify the specified configuration, once previous files have been configured and saved, run the following tool under sequence repository installation directory (changing <version> to specific version )
+In order to verify the specified configuration, once previous files have been configured and saved, run the following tool under sequence repository installation directory :
 On Windows system
 <code>
-java -cp "config;PM-SequenceRepository-<version>.jar;lib\*" fr.proline.module.seq.service.ListMatchingRules
+run-TestConfiguration.bat
 </code>
 On Linux system
 <code>
-java -cp "config:PM-SequenceRepository--<version>.jar:lib/*" fr.proline.module.seq.service.ListMatchingRules
+run-TestConfiguration.sh</code>
+An output will be displayed with all fasta files found and for each which rule will be applied. The first 3 entries of each will also be displayed with the extracted protein accession.
+Output should look like :
+<code>
+ Scanning [D:\temp\fasta]
+ [D:\temp\fasta] scan terminated
+ Number of traversed dirs: 1
+ Found FASTA file names: 7
+  ---- Scanning Fasta local path ----
+  Using default rule ">(\S+)" for fasta "Nouvelle_base_données_sara.fasta"
+ 	 Accession "tr|F8WIX8|H2A.l_MOUSE" will be used for entry ">tr|F8WIX8|H2A.l_MOUSE Original_Name=F8WIX8_MOUSE Histone H2A OS=Mus musculus GN=Hist1h2al PE=3 SV=1".
+ 	 Accession "tr|Q5M8Q2|H2A.L.1.3_MOUSE" will be used for entry ">tr|Q5M8Q2|H2A.L.1.3_MOUSE Original_Name= Q5M8Q2_MOUSE Histone H2A OS=Mus musculus GN=OTTMUSG00000016789 PE=2 SV=1".
+ 	 Accession "tr|J3QP08|H2A.L.1.4_MOUSE" will be used for entry ">tr|J3QP08|H2A.L.1.4_MOUSE Original_Name= J3QP08_MOUSE Histone H2A OS=Mus musculus GN=Gm14501 PE=3 SV=1".
+[UPS1UPS2_D_20121108.fasta] matches Fasta Name Regex "UPS1UPS2_"
+  Using rule ">[^\|]*\|(\S+)" for "UPS1UPS2_D_20121108.fasta"
+    Release (using rule "_(?:D|(?:Decoy))_(.*)\.fasta") = "20121108"
+ 	 Accession "ALBU_HUMAN_UPS" will be used for entry ">P02768ups|ALBU_HUMAN_UPS Serum albumin (Chain 26-609) - Homo sapiens (Human)".
+ 	 Accession "NEDD8_HUMAN_UPS" will be used for entry ">Q15843ups|NEDD8_HUMAN_UPS NEDD8 (Chain 1-81) - Homo sapiens (Human)".
+ 	 Accession "RASH_HUMAN_UPS" will be used for entry ">P01112ups|RASH_HUMAN_UPS GTPase HRas (Chain 1-189) - Homo sapiens (Human)".
+  Using default rule ">(\S+)" for fasta "uniprot-taxonomy%3A-Mus+musculus+%28Mouse%29+%5B10090%5D-.fasta"
+ 	 Accession "sp|Q9CQV8|1433B_MOUSE" will be used for entry ">sp|Q9CQV8|1433B_MOUSE 14-3-3 protein beta/alpha OS=Mus musculus GN=Ywhab PE=1 SV=3".
+ 	 Accession "sp|P62259|1433E_MOUSE" will be used for entry ">sp|P62259|1433E_MOUSE 14-3-3 protein epsilon OS=Mus musculus GN=Ywhae PE=1 SV=1".
+ 	 Accession "sp|P68510|1433F_MOUSE" will be used for entry ">sp|P68510|1433F_MOUSE 14-3-3 protein eta OS=Mus musculus GN=Ywhah PE=1 SV=2".
+[iSa_D_20130403.fasta] matches Fasta Name Regex "ISA_"
+  Using rule ">\w{2}\|([^\|]+)\|" for "iSa_D_20130403.fasta"
+    Release (using rule "_(?:D|(?:Decoy))_(.*)\.fasta") = "20130403"
+ 	 Accession "Q99M51tag" will be used for entry ">sp|Q99M51tag|NCK1_strep-tag Cytoplasmic protein NCK1 OS=Mus musculus GN=Nck1 PE=1 SV=1".
+ 	 Accession "Q9ES52tag" will be used for entry ">sp|Q9ES52tag|SHIP1_strep-tag Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 OS=Mus musculus GN=Inpp5d PE=1 SV=2".
+ 	 Accession "###REV###Q99M51tag" will be used for entry ">sp|###REV###Q99M51tag|NCK1_strep-tag Reverse sequence, was Cytoplasmic protein NCK1 OS=Mus musculus GN=Nck1 PE=1 SV=1".
+[UP_MouseEDyP_D_20150629.fasta] matches Fasta Name Regex "UP_"
+  Using rule ">\w{2}\|([^\|]*)\|\S+" for "UP_MouseEDyP_D_20150629.fasta"
+    Release (using rule "_([^_])*\.fasta") = "9"
+ 	 Accession "Q9CQV8" will be used for entry ">sp|Q9CQV8|1433B_MOUSE 14-3-3 protein beta/alpha OS=Mus musculus GN=Ywhab PE=1 SV=3".
+ 	 Accession "Q9CQV8-2" will be used for entry ">sp|Q9CQV8-2|1433B_MOUSE Isoform Short of 14-3-3 protein beta/alpha OS=Mus musculus GN=Ywhab".
+ 	 Accession "P62259" will be used for entry ">sp|P62259|1433E_MOUSE 14-3-3 protein epsilon OS=Mus musculus GN=Ywhae PE=1 SV=1".
+[S_cerevisiae_Decoy_20121108.fasta] matches Fasta Name Regex "S_cerevisiae_"
+  Using rule ">\w{2}\|([^\|]*)\|\S+" for "S_cerevisiae_Decoy_20121108.fasta"
+    Release (using rule "_([^_])*\.fasta") = "8"
+ 	 Accession "P38903" will be used for entry ">sp|P38903|2A5D_YEAST Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RTS1 PE=1 SV=2".
+ 	 Accession "P31383" will be used for entry ">sp|P31383|2AAA_YEAST Protein phosphatase PP2A regulatory subunit A OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TPD3 PE=1 SV=3".
+ 	 Accession "Q00362" will be used for entry ">sp|Q00362|2ABA_YEAST Protein phosphatase PP2A regulatory subunit B OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CDC55 PE=1 SV=2".
+[UPS1UPS2_Decoy_20121108.fasta] matches Fasta Name Regex "UPS1UPS2_"
+  Using rule ">[^\|]*\|(\S+)" for "UPS1UPS2_Decoy_20121108.fasta"
+    Release (using rule "_(?:D|(?:Decoy))_(.*)\.fasta") = "20121108"
+ 	 Accession "ALBU_HUMAN_UPS" will be used for entry ">P02768ups|ALBU_HUMAN_UPS Serum albumin (Chain 26-609) - Homo sapiens (Human)".
+ 	 Accession "NEDD8_HUMAN_UPS" will be used for entry ">Q15843ups|NEDD8_HUMAN_UPS NEDD8 (Chain 1-81) - Homo sapiens (Human)".
+ 	 Accession "RASH_HUMAN_UPS" will be used for entry ">P01112ups|RASH_HUMAN_UPS GTPase HRas (Chain 1-189) - Homo sapiens (Human)".
+</code>
+===== Running Sequence Repository =====
+To run Sequence Repository, you should modify and execute
+On Windows system
+<code>
+run-RetrieveService.bat
+</code>
+On Linux system
+<code>
+run-RetrieveService.sh
 </code>
+By default, RetrieveService will be run with option "-t 2" : daemon will be executed every 2 hours. To modify the option, edit the run-RetrieveService script file and change option after fr.proline.module.seq.service.RetrieveService string.
+Available option are:
+Usage: <main class> [options]
+  Options:
+    -f, --forceUpdate
+       force update of MSIdb result summaries and biosequences (even if already
+       updated)
+       Default: false
+    -p, --project
+       the ID of the single project to process
+       Default: 0
+    -t, --time
+       the daemon periodicity (in hours)
+       Default: -1
+    -debug
+       set logger level to DEBUG (verbose mode)
+       Default: false

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