Differences

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--- pgd_spider_-_manual [2011/10/11 15:41] – heidi
+++ pgd_spider_-_manual [2012/05/07 09:11] (current) – heidi
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 ====== PGDSpider Manual ======
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-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]]\\
+\\
+===== 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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   * **Windows:** execute the command ''PGDSpider2-cli.exe''
   * **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>**:
     * 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.
   * **-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.
-    * 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.
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   * “example_SAM.sam” and its reference file “example_SAM_references.fasta”:
     * 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”:
     * 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.