Ensembl installation - Revision history

Ivan@dote.ru: /* Notes */

2018-10-24T06:58:57Z

‎Notes

Ivan@dote.ru: /* Notes */

2018-10-24T06:58:35Z

‎Notes

Ivan@dote.ru: /* Notes */

2018-10-24T06:47:16Z

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Ivan@dote.ru: /* Notes */

2018-10-24T06:44:28Z

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Ivan@dote.ru: /* Notes */

2018-07-26T09:34:20Z

‎Notes

Ivan@dote.ru at 07:19, 16 March 2018

2018-03-16T07:19:13Z

Ivan@dote.ru at 06:01, 16 March 2018

2018-03-16T06:01:19Z

Lan@dote.ru: commons-net-3.2.jar -> commons-net-3.3.jar

2013-06-13T06:55:29Z

commons-net-3.2.jar -> commons-net-3.3.jar

Lan@dote.ru: /* Notes */

2013-06-11T11:04:16Z

‎Notes

Lan@dote.ru: Created page with "This page describes how to install Ensembl database and integrate it with BioUML server or BioUML workbench. The information described here is valid for BioUML 0.9.5 a..."

2013-06-11T11:04:02Z

Created page with "This page describes how to install Ensembl database and integrate it with BioUML server or BioUML workbench. The information described here is valid for BioUML 0.9.5 a..."

New page

This page describes how to install Ensembl database and integrate it with [[BioUML server]] or [[BioUML workbench]]. The information described here is valid for BioUML 0.9.5 and higher.

* Go to BioUML src directory/db_setup/ensembl
* Edit build.xml there:
** SPECIES: lower-case underscore-separated taxonomical species (homo_sapiens, mus_musculus or rattus_norvegicus)
** VERSION: underscore-separated Ensembl release version for given species (like '71_37'). Visit ftp://ftp.ensembl.org/pub/current_mysql/ to check the latest version available (it's the suffix of the corresponding directory name).
** GENOME_BUILD: Genome build string like 'hg19' or 'mm10'. Leave this empty if you're not sure.
** COLLECTION_NAME: How the resulting database will be named in BioUML installation under 'databases' tab.
** SOURCE_FOLDER: Folder to store downloaded files. Default is "." which means the current folder.
** TARGET_PATH: Path to 'databases' root of BioUML [[repository]]. Usually it's a subfolder inside the BioUML installation folder, named 'repo' for [[BioUML server]] and 'data' for [[BioUML workbench]].
** DB_HOST: mysql server host to connect to.
** USER, PASS: mysql user and password with administrative privileges.
* Put commons-net-3.2.jar into ant CLASSPATH. See [http://ant.apache.org/manual/install.html Ant installation manual] for details.
* Run ant (with default target “setup”).

=== Notes ===
#Default target will do the following things:
#* Download necessary database dumps;
#* Create mysql databases named in the same was as in the Ensembl (for example, "homo_sapiens_core_71_37");
#* Grant an access to these databases to user 'ensembl' with password 'ensembl';
#* Create schema and import database dumps;
#* Create repository configuration files.

#If necessary, you may use separate ant targets for downloading, installing or creating configuration files.

#Make sure that created configuration files in repository are accessible for the user which will be used for running BioUML.

#Lucene indexes should be created separately for installed Ensembl. See [[Lucene indexes creation]] for details.

[[Category:Installation]]

@@ Line 27: / Line 27: @@
 #If you use mysql version > 5.6 you should enable compatibility with MySQL 5.6 (version used by ensembl to create dumps). Run in mysql console:
 <code>set GLOBAL show_compatibility_56 = ON</code>
 <code>SET GLOBAL sql_mode = '';</code>
 [[Category:Installation]]

@@ Line 27: / Line 27: @@
 #If you use mysql version > 5.6 you should enable compatibility with MySQL 5.6 (version used by ensembl to create dumps). Run in mysql console:
 <code>set GLOBAL show_compatibility_56 = ON</code>
-#for newer mysql versions replcate datetime default values:
+<code>SET GLOBAL sql_mode = '';</code>
 <code>
-<nowiki>
-sed -i "s/'0000-00-00 00:00:00'/CURRENT_TIMESTAMP/g" build.xml;
-for f in */*.sql.gz; do
-  echo $f;
-  zcat $f | sed "s/'0000-00-00 00:00:00'/CURRENT_TIMESTAMP/g" | gzip -c > ${f}.tmp;
-  mv ${f}.tmp $f;
-done
-</nowiki>
 </code>
 [[Category:Installation]]

@@ Line 29: / Line 29: @@
 #for newer mysql versions replcate datetime default values:
 <code>
-sed -i "s/'0000-00-00 00:00:00'/CURRENT_TIMESTAMP/g" build.xml
+<nowiki>
 for f in */*.sql.gz; do
    echo $f;
@@ Line 35: / Line 36: @@
    mv ${f}.tmp $f;
 done
-<code>
+</nowiki>
 [[Category:Installation]]

@@ Line 27: / Line 27: @@
 #If you use mysql version > 5.6 you should enable compatibility with MySQL 5.6 (version used by ensembl to create dumps). Run in mysql console:
 <code>set GLOBAL show_compatibility_56 = ON</code>
 [[Category:Installation]]

@@ Line 26: / Line 26: @@
 #Lucene indexes should be created separately for installed Ensembl. See [[Lucene indexes creation]] for details.
 #If you use mysql version > 5.6 you should enable compatibility with MySQL 5.6 (version used by ensembl to create dumps). Run in mysql console:
-<code>show_compatibility_56 = ON</code>
+<code>set GLOBAL show_compatibility_56 = ON</code>
 [[Category:Installation]]

@@ Line 13: / Line 13: @@
 * Put commons-net-3.3.jar into ant CLASSPATH. See [http://ant.apache.org/manual/install.html Ant installation manual] for details.
 * Run ant (with default target “setup”).
 === Notes ===

@@ Line 11: / Line 11: @@
 ** DB_HOST: mysql server host to connect to.
 ** USER, PASS: mysql user and password with administrative privileges.
-* Put commons-net-3.2.jar into ant CLASSPATH. See [http://ant.apache.org/manual/install.html Ant installation manual] for details.
+* Put commons-net-3.3.jar into ant CLASSPATH. See [http://ant.apache.org/manual/install.html Ant installation manual] for details.
 * Run ant (with default target “setup”).

@@ Line 21: / Line 21: @@
 #* Create schema and import database dumps;
 #* Create repository configuration files.
 #If necessary, you may use separate ant targets for downloading, installing or creating configuration files.
 #Make sure that created configuration files in repository are accessible for the user which will be used for running BioUML.
 #Lucene indexes should be created separately for installed Ensembl. See [[Lucene indexes creation]] for details.
 [[Category:Installation]]