PASA - Revision history

Rf at 16:54, 24 November 2017

2017-11-24T16:54:02Z

Rf at 16:47, 24 November 2017

2017-11-24T16:47:31Z

Rf: Created page with "= Introduction = Brian Haas also behind this Splice Alignment tool. = Installation = * The PASA mysql user requires full privileges so it can create databases, which it app..."

2017-11-24T16:40:19Z

Created page with "= Introduction = Brian Haas also behind this Splice Alignment tool. = Installation = * The PASA mysql user requires full privileges so it can create databases, which it app..."

New page

= Introduction =

Brian Haas also behind this Splice Alignment tool.

= Installation =

* The PASA mysql user requires full privileges so it can create databases, which it apparently does for every analysis.
* these privileges must also exist for '%', so that all the nodes can also do this.
* the issue of a key being too long for mysql was corrected by replacing 1000 with 500 in this line.

gene_id varchar(1000) default NULL,

in the $PASAHOME/schema/cdna_alignment_mysqlschema file on line 174, which was also an issue back in 2013 (see links section).

= Links =

* Yours truly posing a question in May 2013! [https://sourceforge.net/p/pasa/mailman/message/30827159 here].

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 = Using PASA =
-PASA has quite alot of parts and it could almost be seen as a mini-pipeline. THe canonical command for running it on the marvin cluster is:
+PASA has quite alot of parts and it could almost be seen as a mini-pipeline. Therefore the user needs to read the documentation well to use the software properly. Please see the links section for PASA's main documentation page.
   Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g genome_sample.fasta -t all_transcripts.fasta.clean -T -u all_transcripts.fasta -f FL_accs.txt --ALIGNERS blat,gmap --CPU 2
@@ Line 24: / Line 26: @@
 =  Links =
+* Pasa's main documentation page is [https://pasapipeline.github.io here].
 * Yours truly posing a question in May 2013! [https://sourceforge.net/p/pasa/mailman/message/30827159 here].

← Older revision		Revision as of 16:47, 24 November 2017
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	Brian Haas also behind this Splice Alignment tool.		Brian Haas also behind this Splice Alignment tool.
		+
		+	= Using PASA =
		+
		+	PASA has quite alot of parts and it could almost be seen as a mini-pipeline. THe canonical command for running it on the marvin cluster is:
		+
		+	Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g genome_sample.fasta -t all_transcripts.fasta.clean -T -u all_transcripts.fasta -f FL_accs.txt --ALIGNERS blat,gmap --CPU 2
		+	<ins>Explanation</ins>:
		+	* '''-c''' is a configuration file which you, the user, needs to set up. The database name you choose for the analysis needs to be specified in this.
		+	* '''-C''' is for creating a new database, if there is one there already, the command will fail.
		+	* '''--CPU''' is for the number of threads.

	= Installation =		= Installation =