Stacks - Revision history

Jw297: /* Installation and compilation (admins only) */

2018-04-04T10:03:44Z

‎Installation and compilation (admins only)

2016-07-28T13:11:29Z

2016-05-17T14:53:55Z

‎Example command-lines

2016-05-17T14:47:06Z

2016-05-17T14:37:16Z

2016-05-17T14:35:41Z

2016-05-17T14:30:44Z

2016-05-17T14:29:33Z

2016-05-17T14:13:32Z

2016-05-10T15:07:51Z

← Older revision		Revision as of 10:03, 4 April 2018
Line 62:		Line 62:

	The settings in these files referring to the mysql server should be modified appropriately.		The settings in these files referring to the mysql server should be modified appropriately.
		+
		+	Installing stacks 2.0b7 and 2.0b9 sucked. This magic from Ramon worked:
		+	./configure CXX=/usr/local/Modules/modulefiles/tools/gcc/4.9.3/bin/g++ CPP='/usr/local/Modules/modulefiles/tools/gcc/4.9.3/bin/g++ -E' --prefix=whatever

@@ Line 54: / Line 54: @@
 Stacks uses the usual '''configure && make && make install''' routine, but has several configure options. Primarily there is bam: this is not precisely bamtools, but rather samtools, though the directories say bam and not samtools ... the documentation isn't very clear. In any case, this is a model of a workable compile line.
-  ./configure --enable-bam --with-bam-include-path=/usr/local/include/bam --with-bam-lib-path=/usr/local/lib
+  ./configure --prefix=/usr/local/Modules/modulefiles/tools/stacks/1.41 --enable-bam --enable-sparsehash --with-bam-include-path=/usr/local/Modules/modulefiles/        tools/sa
 The Stacks installation itself then needs a further two modifications which will make it depend on a particular running mysql server. It does seem to be the case that only one mysql server can be used for one Stacks installation, by the nature of these two modifications. The files to be modified are:

@@ Line 28: / Line 28: @@
 <ins>Explanation:</ins>
 * -P, an input path, containing the previous Stacks' command output.
 * -M, the input population map.
 * -m, -r these are settings, the minimum stack depth for individuals and the minimum percentage of individuals in a population, respectively, at a locus.
 = setting up database on mysql =

@@ Line 30: / Line 30: @@
 * -P, an input path, containing the previous Stacks' command output.
 * -M, the input population map.
 = setting up database on mysql =
 * Create database, you must have the appropriate privileges for this. If you do, the command will be something like:

@@ Line 28: / Line 28: @@
 <ins>Explanation:</ins>
 * -M, the input population map.
 = setting up database on mysql =

@@ Line 17: / Line 17: @@
   process_radtags -p ./raw/ -b ./barcodes/barcodes_lane3 -e sbfI -o ./samples/ -r -c -q
-<ins>Explanation</ins>
+<ins>Explanation:</ins>
 * -p, -b and -e are inputs, the directory with the fastq reads, the barcode file and the name of the restriction enzyme used.
 * -r -c -q: these clean the data and correct barcodes and restriction enzyme cutsites.
 * -o if for the directory in which to hold the output
 = setting up database on mysql =
 * Create database, you must have the appropriate privileges for this. If you do, the command will be something like:

@@ Line 15: / Line 15: @@
 == Typical workflow ==
-process_radtags -p ./raw/ -e sbfI -b ./barcodes/barcodes_lane3 -o ./samples/ -r -c -q
+ process_radtags -p ./raw/ -e sbfI -b ./barcodes/barcodes_lane3 -o ./samples/ -r -c -q
 <ins>Explanation</ins>

@@ Line 13: / Line 13: @@
 * Either the '''populations''' or '''genotypes''' program is executed, depending on input datasets,
-== setting up database on mysql ==
+== Typical workflow ==
 * Create database, you must have the appropriate privileges for this. If you do, the command will be something like:
   echo "CREATE DATABASE <mynewdbname>" | mysql -h <name_of_server_running_mysql> -u <myusername> -p

← Older revision		Revision as of 15:07, 10 May 2016
Line 32:		Line 32:

	./configure --enable-bam --with-bam-include-path=/usr/local/include/bam --with-bam-lib-path=/usr/local/lib		./configure --enable-bam --with-bam-include-path=/usr/local/include/bam --with-bam-lib-path=/usr/local/lib
		+
		+	The Stacks installation itself then needs a further two modifications which will make it depend on a particular running mysql server. It does seem to be the case that only one mysql server can be used for one Stacks installation, by the nature of these two modifications. The files to be modified are:
		+	* <stack_root_dir>/share/stacks/php/constants.php
		+	* <stack_root_dir>/share/stacks/sql/mysql.cnf
		+
		+	The settings in these files referring to the mysql server should be modified appropriately.