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pgd_spider_-_manual [2011/10/11 15:41] – heidipgd_spider_-_manual [2012/05/07 09:11] (current) – heidi
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 ====== PGDSpider Manual ====== ====== PGDSpider Manual ======
 {{splashscreen.png|}}\\ {{splashscreen.png|}}\\
-PGDSpider version 2.0.1.0 (October 2011)+PGDSpider version 2.0.1.6 (May 2012)
  
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 PGDSpider is written in Java and therefore platform independent, but SUN Java 1.6 RE (or a newer version) has to be installed. Java6 RE can be downloaded under following link:[[http://www.oracle.com/technetwork/java/javase/downloads/index.html]]\\ PGDSpider is written in Java and therefore platform independent, but SUN Java 1.6 RE (or a newer version) has to be installed. Java6 RE can be downloaded under following link:[[http://www.oracle.com/technetwork/java/javase/downloads/index.html]]\\
    
 +\\
 +
 +===== Java Web Start: =====
 +Additionally we provide the possibility to download and run PGDSpider from the web by the Java Web Start software. Java Web Start provides an easy, one-click activation of PGDSpider and it guarantees that you are always running the latest version.
 +
 +\\
 +
 +
 +
 +==== Launch PGDSpider ====
 +Java Web Start is included in the [[http://www.oracle.com/technetwork/java/javase/downloads/index.html|Java Runtime Environment]].\\
 +\\
 +Launch PGDSpider using Java Web Start from:
 +  * **Browser:** Click on following PGDSpider Web Start icon: [[http://www.cmpg.unibe.ch/software/PGDSpider/jnlp/PGDSpider2.jnlp|{{webstart_btn_3.png}}]]
 +  * **Java Cache Viewer:** To launch the PGDSpider Web Start a second time, you do not need to return to the web page where you first launched it; instead you can launch it from the Java Cache Viewer. To open the Java Cache Viewer execute following command in the console: ''javaws -viewer''. To run PGDSpider Web Start, select it and click the Run button or double click the PGDSpider application.
 +  * **Desktop:** You can add a desktop shortcut to the PGDSpider Web Start application. Select the application in the Java Cache Viewer (see above how to open it), then right-click and select “Install Shortcuts” or click the Install button. A shortcut is added to the desktop and you can launch the PGDSpider Web Start application just as you would launch any native application.
 +
 +\\
 +
 +==== Limitations ====
 +Starting PGDSpider from Java Web Start it is not possible to change the amount of memory PGDSpider is allowed to use (by default it is set to 1 GB). If you need to change the amount of memory (e.g.: if you have large files to convert), download the PGDSpider application as described in the 2nd step of the [[http://www.cmpg.unibe.ch/software/PGDSpider/#Download_and_Installation_Instructions|Installation Instructions]] on the web page.
 +
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   * **Select a SPID file:** Click on the button “Select SPID file” to select a SPID file which contains the answers for the Parser and the Writer Questions.   * **Select a SPID file:** Click on the button “Select SPID file” to select a SPID file which contains the answers for the Parser and the Writer Questions.
   * **Drop SPID file:** Click on the button “Drop SPID file” to remove the selected SPID file.   * **Drop SPID file:** Click on the button “Drop SPID file” to remove the selected SPID file.
-  * **Create/Edit SPID file:**Click on the button “Create/Edit SPID file” to open a window with the SPID editor to create or edit a SPID file.+  * **Create/Edit SPID file:** Click on the button “Create/Edit SPID file” to open a window with the SPID editor to create or edit a SPID file.
   * **Convert file format:** To convert the specified input file to the desired output format, press the “Convert” button. If no SPID file was selected a window appear with Parser and Writer questions (SPID editor). When the questions are answered, the user has the possibility to save the answers in a SPID file. Afterwards the answers are applied in the conversion process. A progress bar at the bottom of the graphical user interface shows the progress of the parsing action. After conversion, the user should control the output file (mistakes in the input file could lead to mistakes in the output file)!    * **Convert file format:** To convert the specified input file to the desired output format, press the “Convert” button. If no SPID file was selected a window appear with Parser and Writer questions (SPID editor). When the questions are answered, the user has the possibility to save the answers in a SPID file. Afterwards the answers are applied in the conversion process. A progress bar at the bottom of the graphical user interface shows the progress of the parsing action. After conversion, the user should control the output file (mistakes in the input file could lead to mistakes in the output file)! 
   * **View the output file:** If conversion is over, one can have a look at the generated output file if the button “view file” in the Output File area is clicked.   * **View the output file:** If conversion is over, one can have a look at the generated output file if the button “view file” in the Output File area is clicked.
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   * **Windows:** execute the command ''PGDSpider2-cli.exe''   * **Windows:** execute the command ''PGDSpider2-cli.exe''
   * **Linux:** execute the command ''java -Xmx1024m -Xms512m -jar PGDSpider2-cli.jar''   * **Linux:** execute the command ''java -Xmx1024m -Xms512m -jar PGDSpider2-cli.jar''
-  * **Other:** execute the command ''java -Xmx1024m -Xms512m -jar PGDSpider2-cli.jar''+  * **Mac and others:** execute the command ''java -Xmx1024m -Xms512m -jar PGDSpider2-cli.jar''
  
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   * **-inputformat <format>**:    * **-inputformat <format>**: 
     * Specify the format of the input file. This option is mandatory if the input format is not defined in the answer (SPID) file.     * Specify the format of the input file. This option is mandatory if the input format is not defined in the answer (SPID) file.
-    * Possible input formats are: PGD, ARLEQUIN, BAM, BAPS, BATWING, BCF, CONVERT, FASTA, FSTAT, GDA, GENELAND, GENEPOP, GENETIX, HGDP_CEPH, IMMANC, IM, MEGA, MIGRATE, MSA, NEWHYBRIDS, NEXUS, PED, PHYLIP, SAM, STRUCTURE, VCF+    * Possible input formats are: PGD, ARLEQUIN, BAM, BAPS, BATWING, BCF, CONVERT, FASTA, FASTQ, FSTAT, GDA, GENELAND, GENEPOP, GENETIX, HGDP_CEPH, IMMANC, IM, MEGA, MIGRATE, MSA, NEWHYBRIDS, NEXUS, PED, PHYLIP, SAM, STRUCTURE, VCF
   * **-outputfile <file>** (mandatory): Specify the output file for the conversion process.   * **-outputfile <file>** (mandatory): Specify the output file for the conversion process.
   * **-outputformat <format>**:   * **-outputformat <format>**:
     * Specify the format of the output file. This option is mandatory if the output format is not defined in the answer (SPID) file.     * Specify the format of the output file. This option is mandatory if the output format is not defined in the answer (SPID) file.
-    * Possible output formats are: PGD, ARLEQUIN, BAM, BAPS, BATWING, BCF, FASTA, FDIST2, FSTAT, GDA, GENELAND, GENEPOP, GENETIX, GESTE_BAYE_SCAN, IMMANC, IM, KML, MEGA, MIGRATE, MSA, MSVAR, NEWHYBRIDS, NEXUS, PED, PHYLIP, SAM, STRUCTURE, VCF+    * Possible output formats are: PGD, ARLEQUIN, BAM, BAPS, BATWING, BCF, FASTA, FASTQ, FDIST2, FSTAT, GDA, GENELAND, GENEPOP, GENETIX, GESTE_BAYE_SCAN, IMMANC, IM, KML, MEGA, MIGRATE, MSA, MSVAR, NEWHYBRIDS, NEXUS, PED, PHYLIP, SAM, STRUCTURE, VCF
   * **-spid <file>** (mandatory): Specify the SPID file containing the preanswered conversion questions. The SPID file can be generated with the help of the SPID Editor integrated in the PGDSpider GUI.   * **-spid <file>** (mandatory): Specify the SPID file containing the preanswered conversion questions. The SPID file can be generated with the help of the SPID Editor integrated in the PGDSpider GUI.
  
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   * “example_SAM.sam” and its reference file “example_SAM_references.fasta”:   * “example_SAM.sam” and its reference file “example_SAM_references.fasta”:
     * Data: NGS, diploid     * Data: NGS, diploid
-    * Convert to: [[Arlequin]], [[http://phd.chnebu.ch/index.php/SAMtools#BAM_format|BAM]], [[BAPS]], [[http://phd.chnebu.ch/index.php/Variant_Call_Format_(VCF)#Binary_variant_Call_Format_.28BCF.29|BCF]], [[FASTA]], [[FDist2]], [[GENELAND]], [[MEGA]], [[MIGRATE]], [[NEXUS]], [[PGD]], [[PHYLIP]], [[http://phd.chnebu.ch/index.php/SAMtools|SAM]], [[http://phd.chnebu.ch/index.php/Variant_Call_Format_(VCF)|VCF]]+    * Convert to: [[Arlequin]], [[http://phd.chnebu.ch/index.php/SAMtools#BAM_format|BAM]], [[BAPS]], [[http://phd.chnebu.ch/index.php/Variant_Call_Format_(VCF)#Binary_variant_Call_Format_.28BCF.29|BCF]], [[FASTA]], [[FASTQ]], [[FDist2]], [[GENELAND]], [[MEGA]], [[MIGRATE]], [[NEXUS]], [[PGD]], [[PHYLIP]], [[http://phd.chnebu.ch/index.php/SAMtools|SAM]], [[http://phd.chnebu.ch/index.php/Variant_Call_Format_(VCF)|VCF]]
   * “example_Structure.txt”:   * “example_Structure.txt”:
     * Data: Microsat (as number of repeats), diploid (on two consecutive rows), “Phase Information” row is not present, Missing value code = -9, “Locus names” are present, “individual labels” are present, “PopData” column is present, “Recessive Alleles/Inter-Marker Distance” rows are not present.     * Data: Microsat (as number of repeats), diploid (on two consecutive rows), “Phase Information” row is not present, Missing value code = -9, “Locus names” are present, “individual labels” are present, “PopData” column is present, “Recessive Alleles/Inter-Marker Distance” rows are not present.
pgd_spider_-_manual.1318340469.txt.gz · Last modified: 2011/10/11 15:41 by heidi