Difference between revisions of "WebApollo Tutorial 2013"
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These are the steps I took to install WebApollo on the prebuilt AWS image. Some steps need only be performed once, such as installing the custom valves in Tomcat or installing BLAT, to ensure that the system is ready. These steps will be denoted with an asterisk (*). | These are the steps I took to install WebApollo on the prebuilt AWS image. Some steps need only be performed once, such as installing the custom valves in Tomcat or installing BLAT, to ensure that the system is ready. These steps will be denoted with an asterisk (*). | ||
− | Note: These notes follow along with the general WebApollo installation guide ( | + | Note: These notes follow along with the general WebApollo installation guide (). The guide below details the steps I used to set up the GMOD Summer School 2013 AMI. |
For more information about using WebApollo, please see the user guide, located here: http://genomearchitect.org/webapollo/docs/webapollo_user_guide.pdf | For more information about using WebApollo, please see the user guide, located here: http://genomearchitect.org/webapollo/docs/webapollo_user_guide.pdf | ||
− | + | ==Prerequisites== | |
− | =Prerequisites= | + | |
* * Install Tomcat7* | * * Install Tomcat7* | ||
* * Install BLAT/verify location* | * * Install BLAT/verify location* | ||
* * PostgreSQL is installed and configured* | * * PostgreSQL is installed and configured* | ||
* * Download WebApollo (and sample data)* | * * Download WebApollo (and sample data)* | ||
− | + | mkdir ~/dataHome/WebApollo2 | |
− | + | cd ~/dataHome/WebApollo2 | |
− | + | wget https://apollo-web.googlecode.com/files/WebApollo-2013-05-16.tgz | |
− | + | wget http://genomearchitect.org/webapollo/data/pyu_data.tgz | |
− | + | tar -xvzf WebApollo-2013-05-16.tgz | |
− | + | tar -xvzf pyu_data.tgz | |
− | + | ||
− | =Database Setup= | + | ==Database Setup== |
* Create PostgreSQL user with proper permissions for WebApollo to use | * Create PostgreSQL user with proper permissions for WebApollo to use | ||
$ sudo su postgres | $ sudo su postgres | ||
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* Create a database for managing the WebApollo users | * Create a database for managing the WebApollo users | ||
$ createdb -U web_apollo_users_admin web_apollo_users | $ createdb -U web_apollo_users_admin web_apollo_users | ||
+ | $ exit | ||
* Populate the database with the WebApollo User schema | * Populate the database with the WebApollo User schema | ||
− | + | cd /data/dataHome/WebApollo2/WebApollo-2013-05-16/tools/user | |
− | + | psql -U web_apollo_users_admin web_apollo_users < \ | |
user_database_postgresql.sql | user_database_postgresql.sql | ||
* Create a user with access to WebApollo | * Create a user with access to WebApollo | ||
− | + | ./add_user.pl -D web_apollo_users -U web_apollo_users_admin -P \ | |
web_apollo_users_admin -u web_apollo_admin -p web_apollo_admin | web_apollo_users_admin -u web_apollo_admin -p web_apollo_admin | ||
* The database is ready and has an initial user, which we will use as an administrator. | * The database is ready and has an initial user, which we will use as an administrator. | ||
* We now need to add in the sequences and grant permissions to the user we just created. | * We now need to add in the sequences and grant permissions to the user we just created. | ||
− | + | cd /data/dataHome/WebApollo2/WebApollo-2013-05-16/tools/user | |
− | + | mkdir /data/dataHome/WebApollo2/pyu_data/scratch/ | |
− | + | ./extract_seqids_from_fasta.pl -p Annotations- \ | |
− | + | -i /data/dataHome/WebApollo2/pyu_data/scf1117875582023.fa \ | |
+ | -o /data/dataHome/WebApollo2/pyu_data/scratch/seqids.txt | ||
* Add those ids to the user database. | * Add those ids to the user database. | ||
+ | cd /data/dataHome/WebApollo2/WebApollo-2013-05-16/tools/user | ||
+ | ./add_tracks.pl -D web_apollo_users -U web_apollo_users_admin \ | ||
+ | -P web_apollo_users_admin -t /data/dataHome/WebApollo2/pyu_data/scratch/seqids.txt | ||
− | |||
− | |||
− | |||
− | |||
− | |||
* Now that we have created the user and have loaded the annotation track ids, we’ll need to give the user | * Now that we have created the user and have loaded the annotation track ids, we’ll need to give the user | ||
* permissions to access the sequence. We’ll have the all permissions (read, write, publish, user manager). | * permissions to access the sequence. We’ll have the all permissions (read, write, publish, user manager). | ||
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* of genomic sequence ids, like in the previous step. | * of genomic sequence ids, like in the previous step. | ||
− | + | cd /data/dataHome/WebApollo2/WebApollo-2013-05-16/tools/user | |
− | web_apollo_users_admin -P web_apollo_users_admin - | + | ./set_track_permissions.pl -D web_apollo_users \ |
− | web_apollo_admin -t | + | –U web_apollo_users_admin -P web_apollo_users_admin -a \ |
− | + | -u web_apollo_admin -t /data/dataHome/WebApollo2/pyu_data/scratch/seqids.txt | |
− | + | ||
+ | ==Update Tomcat for WebApollo== | ||
* * Install the WebApollo custom valves in the Tomcat7 lib directory* | * * Install the WebApollo custom valves in the Tomcat7 lib directory* | ||
− | + | sudo cp \ | |
− | ~/dataHome/ | + | ~/dataHome/WebApollo2/WebApollo-2013-05-16/tomcat/custom-valves.jar \ |
/usr/share/tomcat7/lib/ | /usr/share/tomcat7/lib/ | ||
Line 79: | Line 74: | ||
* The final file should look like the example below: | * The final file should look like the example below: | ||
− | $ | + | $ less /var/lib/tomcat7/conf/server.xml |
<Host name="localhost" appBase="webapps" | <Host name="localhost" appBase="webapps" | ||
unpackWARs="true" autoDeploy="true" | unpackWARs="true" autoDeploy="true" | ||
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* At this point the server should be ready for WebApollo. | * At this point the server should be ready for WebApollo. | ||
− | =Deploy WebApollo= | + | ==Deploy WebApollo== |
* Create the location for the new instance | * Create the location for the new instance | ||
− | + | sudo mkdir /var/lib/tomcat7/webapps/WebApollo2 | |
− | + | cd /var/lib/tomcat7/webapps/WebApollo2 | |
* Deploy servlet | * Deploy servlet | ||
− | + | sudo jar xvf ~/dataHome/WebApollo2/WebApollo-2013-05-16/war/WebApollo.war | |
* Change ownership of the base WebApollo directory | * Change ownership of the base WebApollo directory | ||
− | + | sudo mkdir /var/lib/tomcat7/webapps/WebApollo2/tmp | |
+ | sudo chown tomcat7:tomcat7 /var/lib/tomcat7/webapps/WebApollo2/tmp | ||
* Tomcat will create a tmp directory to hold exported GFF3, and needs permission to create and modify the contents of that directory. | * Tomcat will create a tmp directory to hold exported GFF3, and needs permission to create and modify the contents of that directory. | ||
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* Once JBrowse and BLAT are set up and configured, we will use this information to finish configuring WebApollo. | * Once JBrowse and BLAT are set up and configured, we will use this information to finish configuring WebApollo. | ||
− | =Data Processing and JBrowse setup= | + | ==Data Processing and JBrowse setup== |
* Create ancillary directories for the new instance | * Create ancillary directories for the new instance | ||
− | + | cd /data/dataHome/WebApollo2 | |
− | + | mkdir Pyu Pyu/Blat Pyu/Blat/tmp Pyu/Annotations Pyu/data | |
* Change ownership to user tomcat7 | * Change ownership to user tomcat7 | ||
− | + | sudo chown -R tomcat7:tomcat7 /data/dataHome/WebApollo2/Pyu/Annotations | |
− | + | sudo chown -R tomcat7:tomcat7 /data/dataHome/WebApollo2/Pyu/Blat/tmp | |
* Set up the JBrowse instance | * Set up the JBrowse instance | ||
− | + | cd /var/lib/tomcat7/webapps/WebApollo2/jbrowse | |
* Create a symbolic link to the large disk where the browser data will be stored | * Create a symbolic link to the large disk where the browser data will be stored | ||
− | + | sudo ln -s /data/dataHome/WebApollo2/Pyu/data/ . | |
* To make loading easier, make another link to the original data directory | * To make loading easier, make another link to the original data directory | ||
− | + | sudo ln -s /data/dataHome/WebApollo2/pyu_data . | |
* WebApollo uses two special tracks, one to display annotations, and one for sequence alterations. We need to copy those from the original downloaded location to the data directory | * WebApollo uses two special tracks, one to display annotations, and one for sequence alterations. We need to copy those from the original downloaded location to the data directory | ||
− | + | cp /data/dataHome/WebApollo2/WebApollo-2013-05-16/json/* ./data/ | |
* Process the data in preparation for loading | * Process the data in preparation for loading | ||
− | + | cd /var/lib/tomcat7/webapps/WebApollo2/jbrowse/pyu_data | |
− | + | mkdir scratch/split_gff | |
* This script splits the Maker output GFF3 file into separate files based on the source | * This script splits the Maker output GFF3 file into separate files based on the source | ||
− | + | ~/dataHome/WebApollo2/WebApollo-2013-05-16/tools/data/split_gff_by_source.pl -i scf1117875582023.gff \ | |
-d scratch/split_gff | -d scratch/split_gff | ||
* Set up the BLAT database | * Set up the BLAT database | ||
− | + | cd /data/dataHome/WebApollo2/Pyu/Blat | |
− | + | ln -s ../../pyu_data/scf1117875582023.fa | |
− | + | faToTwoBit scf1117875582023.fa Pyu.2bit | |
− | + | ==Data Loading== | |
− | =Data Loading= | + | |
* Load the reference sequence(s) and evidence tracks. | * Load the reference sequence(s) and evidence tracks. | ||
* Note: This example uses the results from Maker and simulated BAM and BigWig files. | * Note: This example uses the results from Maker and simulated BAM and BigWig files. | ||
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* Make the scripts in bin/ executable | * Make the scripts in bin/ executable | ||
− | + | cd /var/lib/tomcat7/webapps/WebApollo2/jbrowse | |
+ | sudo chmod +x bin/* | ||
* Load the reference sequence(s) | * Load the reference sequence(s) | ||
− | + | bin/prepare-refseqs.pl --fasta pyu_data/scf1117875582023.fa | |
− | + | ||
* Load the Maker track | * Load the Maker track | ||
bin/flatfile-to-json.pl --gff pyu_data/scratch/split_gff/maker.gff \ | bin/flatfile-to-json.pl --gff pyu_data/scratch/split_gff/maker.gff \ | ||
--arrowheadClass trellis-arrowhead --getSubfeatures \ | --arrowheadClass trellis-arrowhead --getSubfeatures \ | ||
− | --subfeatureClasses '{"wholeCDS": null, "CDS":"brightgreen-80pct", | + | --subfeatureClasses '{"wholeCDS": null, "CDS":"brightgreen-80pct", "UTR": "darkgreen-60pct", "exon":"container-100pct"}' \ |
− | + | ||
--cssClass container-16px --type mRNA --trackLabel maker \ | --cssClass container-16px --type mRNA --trackLabel maker \ | ||
− | --webApollo --renderClassName gray-center-20pct | + | --webApollo --renderClassName gray-center-20pct |
+ | |||
* This is a bash script to automate loading the non-Maker tracks. You can either paste it into the command prompt or use it to build a shell script. | * This is a bash script to automate loading the non-Maker tracks. You can either paste it into the command prompt or use it to build a shell script. | ||
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* populate the name hash to generate a searchable list of names | * populate the name hash to generate a searchable list of names | ||
− | + | bin/generate-names.pl | |
* Prepare the BAM data for loading | * Prepare the BAM data for loading | ||
− | + | mkdir data/bam | |
− | + | cp pyu_data/*.bam* data/bam | |
* Load the BAM track | * Load the BAM track | ||
− | + | bin/add_bam_track.pl --bam_url bam/simulated-sorted.bam --label \ | |
simulated_bam --key "simulated BAM" | simulated_bam --key "simulated BAM" | ||
* Prepare the BigWig data for loading | * Prepare the BigWig data for loading | ||
− | + | mkdir data/bigwig | |
− | + | cp pyu_data/*.bw data/bigwig/ | |
* Load the BigWig track | * Load the BigWig track | ||
− | + | bin/add_bw_track.pl --bw_url bigwig/simulated-sorted.coverage.bw \ | |
--label simulated_bw --key "simulated BigWig" | --label simulated_bw --key "simulated BigWig" | ||
* The data for this instance should now be all loaded. | * The data for this instance should now be all loaded. | ||
− | =Final WebApollo configuration | + | ==Final WebApollo configuration== |
* Edit the config.xml file for this instance | * Edit the config.xml file for this instance | ||
* Proper configuration requires us to set several sections of this file to work with our project. | * Proper configuration requires us to set several sections of this file to work with our project. | ||
+ | sudo chown ubuntu:ubuntu * | ||
<!-- directory where JE database will be created --> | <!-- directory where JE database will be created --> | ||
− | <datastore_directory> | + | <datastore_directory>ENTER_DATASTORE_DIRECTORY_HERE</datastore_directory> |
* For this instance, we need to set it to: | * For this instance, we need to set it to: | ||
− | <datastore_directory/data/dataHome/ | + | <datastore_directory>/data/dataHome/WebApollo2/Pyu/Annotations</datastore_directory> |
* Next, edit the user section to connect this instance to the database back end. The database will handle | * Next, edit the user section to connect this instance to the database back end. The database will handle | ||
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<!-- path to JBrowse refSeqs.json file --> <refseqs>ENTER_PATH_TO_REFSEQS_JSON_FILE</refseqs> | <!-- path to JBrowse refSeqs.json file --> <refseqs>ENTER_PATH_TO_REFSEQS_JSON_FILE</refseqs> | ||
* For this instance, we need to set it to: | * For this instance, we need to set it to: | ||
− | <refseqs>/var/lib/tomcat7/webapps/ | + | <refseqs>/var/lib/tomcat7/webapps/WebApollo2/jbrowse/data/refSeqs.json</refseqs> |
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− | * Edit the | + | * Edit the blat_config.xml file for this instance |
<!-- path to Blat binary --> | <!-- path to Blat binary --> | ||
<blat_bin>ENTER_PATH_TO_BLAT_BINARY</blat_bin> | <blat_bin>ENTER_PATH_TO_BLAT_BINARY</blat_bin> | ||
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<!-- path to where to put temporary data --> <tmp_dir>ENTER_PATH_FOR_TEMPORARY_DATA</tmp_dir> | <!-- path to where to put temporary data --> <tmp_dir>ENTER_PATH_FOR_TEMPORARY_DATA</tmp_dir> | ||
* For this instance, we need to set it to: | * For this instance, we need to set it to: | ||
− | <tmp_dir>/data/dataHome/ | + | <tmp_dir>/data/dataHome/WebApollo2/Pyu/Blat/tmp</tmp_dir> |
Line 261: | Line 257: | ||
<database>ENTER_PATH_TO_BLAT_DATABASE</database> | <database>ENTER_PATH_TO_BLAT_DATABASE</database> | ||
* For this instance, we need to set it to: | * For this instance, we need to set it to: | ||
− | <database>/data/dataHome/ | + | <database>/data/dataHome/WebApollo2/Pyu/Blat/Pyu.2bit</database> |
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<blat_options>ENTER_ANY_BLAT_OPTIONS</blat_options> | <blat_options>ENTER_ANY_BLAT_OPTIONS</blat_options> | ||
* For this instance, we need to set it to: | * For this instance, we need to set it to: | ||
− | <blat_options>-minScore=100 -minIdentity=60</blat_options> | + | <blat_options>-minScore=100 -minIdentity=60</blat_options> |
− | + | ==Restart Tomcat== | |
− | =Restart Tomcat= | + | |
* The WebApollo instance should be set up now. | * The WebApollo instance should be set up now. | ||
* Tomcat will need to be restarted for WebApollo to display properly. | * Tomcat will need to be restarted for WebApollo to display properly. | ||
− | + | sudo service tomcat7 restart | |
− | =View your WebApollo instance= | + | ==View your WebApollo instance== |
* You may view your instance by pointing your browser to | * You may view your instance by pointing your browser to | ||
− | http://YOUR _HOST:8080/ | + | http://YOUR _HOST:8080/WebApollo2 |
* To view the site in JBrowse mode use this link format: | * To view the site in JBrowse mode use this link format: | ||
− | http://YOUR _HOST:8080/ | + | http://YOUR _HOST:8080/WebApollo2/jbrowse |
− | =Note on track styling= | + | ==Note on track styling== |
There are several pre-defined track styles included with the WebApollo release. If you'd like to use an included style, replace the subfeature section with the style name: | There are several pre-defined track styles included with the WebApollo release. If you'd like to use an included style, replace the subfeature section with the style name: | ||
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darkorange-60pct | darkorange-60pct | ||
− | + | For example, to style a match type track with light green, adjust the load command like this: | |
+ | |||
--subfeatureClasses "{\"match_part\": \"darkblue-80pct\"}" | --subfeatureClasses "{\"match_part\": \"darkblue-80pct\"}" | ||
Becomes: | Becomes: | ||
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These styles are located in the custom_track_styles.css file: | These styles are located in the custom_track_styles.css file: | ||
− | jbrowse/plugins/ | + | jbrowse/plugins/WebApollo2/css/custom_track_styles.css |
+ | |||
+ | You can also edit the styles after loading. The information on track styles are located in | ||
+ | |||
+ | jbrowse/data/trackList.json | ||
+ | |||
+ | [[Category:WebApollo]] | ||
+ | [[Category:Tutorials]] |
Latest revision as of 00:11, 20 February 2014
These are the steps I took to install WebApollo on the prebuilt AWS image. Some steps need only be performed once, such as installing the custom valves in Tomcat or installing BLAT, to ensure that the system is ready. These steps will be denoted with an asterisk (*).
Note: These notes follow along with the general WebApollo installation guide (). The guide below details the steps I used to set up the GMOD Summer School 2013 AMI.
For more information about using WebApollo, please see the user guide, located here: http://genomearchitect.org/webapollo/docs/webapollo_user_guide.pdf
Contents
Prerequisites
- * Install Tomcat7*
- * Install BLAT/verify location*
- * PostgreSQL is installed and configured*
- * Download WebApollo (and sample data)*
mkdir ~/dataHome/WebApollo2 cd ~/dataHome/WebApollo2 wget https://apollo-web.googlecode.com/files/WebApollo-2013-05-16.tgz wget http://genomearchitect.org/webapollo/data/pyu_data.tgz tar -xvzf WebApollo-2013-05-16.tgz tar -xvzf pyu_data.tgz
Database Setup
- Create PostgreSQL user with proper permissions for WebApollo to use
$ sudo su postgres $ createuser -P web_apollo_users_admin Enter password for new role: Enter it again: Shall the new role be a superuser? (y/n) n Shall the new role be allowed to create databases? (y/n) y Shall the new role be allowed to create more new roles? (y/n) n
- Create a database for managing the WebApollo users
$ createdb -U web_apollo_users_admin web_apollo_users $ exit
- Populate the database with the WebApollo User schema
cd /data/dataHome/WebApollo2/WebApollo-2013-05-16/tools/user psql -U web_apollo_users_admin web_apollo_users < \ user_database_postgresql.sql
- Create a user with access to WebApollo
./add_user.pl -D web_apollo_users -U web_apollo_users_admin -P \ web_apollo_users_admin -u web_apollo_admin -p web_apollo_admin
- The database is ready and has an initial user, which we will use as an administrator.
- We now need to add in the sequences and grant permissions to the user we just created.
cd /data/dataHome/WebApollo2/WebApollo-2013-05-16/tools/user mkdir /data/dataHome/WebApollo2/pyu_data/scratch/ ./extract_seqids_from_fasta.pl -p Annotations- \ -i /data/dataHome/WebApollo2/pyu_data/scf1117875582023.fa \ -o /data/dataHome/WebApollo2/pyu_data/scratch/seqids.txt
- Add those ids to the user database.
cd /data/dataHome/WebApollo2/WebApollo-2013-05-16/tools/user ./add_tracks.pl -D web_apollo_users -U web_apollo_users_admin \ -P web_apollo_users_admin -t /data/dataHome/WebApollo2/pyu_data/scratch/seqids.txt
- Now that we have created the user and have loaded the annotation track ids, we’ll need to give the user
- permissions to access the sequence. We’ll have the all permissions (read, write, publish, user manager).
- We’ll use the set_track_permissions.pl script in the same directory. We’ll need to provide the script a list
- of genomic sequence ids, like in the previous step.
cd /data/dataHome/WebApollo2/WebApollo-2013-05-16/tools/user ./set_track_permissions.pl -D web_apollo_users \ –U web_apollo_users_admin -P web_apollo_users_admin -a \ -u web_apollo_admin -t /data/dataHome/WebApollo2/pyu_data/scratch/seqids.txt
Update Tomcat for WebApollo
- * Install the WebApollo custom valves in the Tomcat7 lib directory*
sudo cp \ ~/dataHome/WebApollo2/WebApollo-2013-05-16/tomcat/custom-valves.jar \ /usr/share/tomcat7/lib/
- * Update the Tomcat7 server.xml to include the WebApollo error reporting VALVE*
- Add errorReportValveClass="org.bbop.apollo.web.ErrorReportValve" as an attribute to the existing <Host> element in: /var/lib/tomcat7/conf/server.xml
- The final file should look like the example below:
$ less /var/lib/tomcat7/conf/server.xml <Host name="localhost" appBase="webapps" unpackWARs="true" autoDeploy="true" errorReportValveClass="org.bbop.apollo.web.ErrorReportValve"> </Host>
- At this point the server should be ready for WebApollo.
Deploy WebApollo
- Create the location for the new instance
sudo mkdir /var/lib/tomcat7/webapps/WebApollo2 cd /var/lib/tomcat7/webapps/WebApollo2
- Deploy servlet
sudo jar xvf ~/dataHome/WebApollo2/WebApollo-2013-05-16/war/WebApollo.war
- Change ownership of the base WebApollo directory
sudo mkdir /var/lib/tomcat7/webapps/WebApollo2/tmp sudo chown tomcat7:tomcat7 /var/lib/tomcat7/webapps/WebApollo2/tmp
- Tomcat will create a tmp directory to hold exported GFF3, and needs permission to create and modify the contents of that directory.
- Once the servlet is deployed we need to configure JBrowse and load the data.
- Once JBrowse and BLAT are set up and configured, we will use this information to finish configuring WebApollo.
Data Processing and JBrowse setup
- Create ancillary directories for the new instance
cd /data/dataHome/WebApollo2 mkdir Pyu Pyu/Blat Pyu/Blat/tmp Pyu/Annotations Pyu/data
- Change ownership to user tomcat7
sudo chown -R tomcat7:tomcat7 /data/dataHome/WebApollo2/Pyu/Annotations sudo chown -R tomcat7:tomcat7 /data/dataHome/WebApollo2/Pyu/Blat/tmp
- Set up the JBrowse instance
cd /var/lib/tomcat7/webapps/WebApollo2/jbrowse
- Create a symbolic link to the large disk where the browser data will be stored
sudo ln -s /data/dataHome/WebApollo2/Pyu/data/ .
- To make loading easier, make another link to the original data directory
sudo ln -s /data/dataHome/WebApollo2/pyu_data .
- WebApollo uses two special tracks, one to display annotations, and one for sequence alterations. We need to copy those from the original downloaded location to the data directory
cp /data/dataHome/WebApollo2/WebApollo-2013-05-16/json/* ./data/
- Process the data in preparation for loading
cd /var/lib/tomcat7/webapps/WebApollo2/jbrowse/pyu_data mkdir scratch/split_gff
- This script splits the Maker output GFF3 file into separate files based on the source
~/dataHome/WebApollo2/WebApollo-2013-05-16/tools/data/split_gff_by_source.pl -i scf1117875582023.gff \ -d scratch/split_gff
- Set up the BLAT database
cd /data/dataHome/WebApollo2/Pyu/Blat ln -s ../../pyu_data/scf1117875582023.fa faToTwoBit scf1117875582023.fa Pyu.2bit
Data Loading
- Load the reference sequence(s) and evidence tracks.
- Note: This example uses the results from Maker and simulated BAM and BigWig files.
- Depending on the data you use in your project, these commands will be different.
- Make the scripts in bin/ executable
cd /var/lib/tomcat7/webapps/WebApollo2/jbrowse sudo chmod +x bin/*
- Load the reference sequence(s)
bin/prepare-refseqs.pl --fasta pyu_data/scf1117875582023.fa
- Load the Maker track
bin/flatfile-to-json.pl --gff pyu_data/scratch/split_gff/maker.gff \ --arrowheadClass trellis-arrowhead --getSubfeatures \ --subfeatureClasses '{"wholeCDS": null, "CDS":"brightgreen-80pct", "UTR": "darkgreen-60pct", "exon":"container-100pct"}' \ --cssClass container-16px --type mRNA --trackLabel maker \ --webApollo --renderClassName gray-center-20pct
- This is a bash script to automate loading the non-Maker tracks. You can either paste it into the command prompt or use it to build a shell script.
for i in $(ls pyu_data/scratch/split_gff/*.gff | grep -v maker); do j=$(basename $i) j=${j/.gff/} echo "Processing $j" bin/flatfile-to-json.pl --gff $i --arrowheadClass webapollo-arrowhead \ --getSubfeatures --subfeatureClasses "{\"match_part\": \"darkblue-80pct\"}" \ --cssClass container-10px --trackLabel $j \ --webApollo --renderClassName gray-center-20pct done
### Output #Processing blastn #Processing blastx #Processing est2genome #Processing protein2genome #Processing repeatmasker #Processing repeatrunner #Processing snap_masked
- populate the name hash to generate a searchable list of names
bin/generate-names.pl
- Prepare the BAM data for loading
mkdir data/bam cp pyu_data/*.bam* data/bam
- Load the BAM track
bin/add_bam_track.pl --bam_url bam/simulated-sorted.bam --label \ simulated_bam --key "simulated BAM"
- Prepare the BigWig data for loading
mkdir data/bigwig cp pyu_data/*.bw data/bigwig/
- Load the BigWig track
bin/add_bw_track.pl --bw_url bigwig/simulated-sorted.coverage.bw \ --label simulated_bw --key "simulated BigWig"
- The data for this instance should now be all loaded.
Final WebApollo configuration
- Edit the config.xml file for this instance
- Proper configuration requires us to set several sections of this file to work with our project.
sudo chown ubuntu:ubuntu *
<datastore_directory>ENTER_DATASTORE_DIRECTORY_HERE</datastore_directory>
- For this instance, we need to set it to:
<datastore_directory>/data/dataHome/WebApollo2/Pyu/Annotations</datastore_directory>
- Next, edit the user section to connect this instance to the database back end. The database will handle
- user accounts, including login authentication and account permissions.
<url>ENTER_USER_DATABASE_JDBC_URL</url>
- For this instance, we need to set it to:
<url>jdbc:postgresql://localhost/web_apollo_users</url>
<username>ENTER_USER_DATABASE_USERNAME</username>
- For this instance, we need to set it to:
<username>web_apollo_users_admin</username>
<password>ENTER_USER_DATABASE_PASSWORD</password>
- For this instance, we need to set it to:
<password>web_apollo_users_admin</password>
<refseqs>ENTER_PATH_TO_REFSEQS_JSON_FILE</refseqs>
- For this instance, we need to set it to:
<refseqs>/var/lib/tomcat7/webapps/WebApollo2/jbrowse/data/refSeqs.json</refseqs>
<organism>ENTER_ORGANISM</organism>
- For this instance, we need to set it to:
<organism>Pythium ultimum</organism>
<sequence_type>ENTER_CVTERM_FOR_SEQUENCE</sequence_type>
- This is formatted “CV:term”, and may change depending on your reference assembly.
<sequence_type>sequence:contig</sequence_type>
- Edit the blat_config.xml file for this instance
<blat_bin>ENTER_PATH_TO_BLAT_BINARY</blat_bin>
- For this instance, we need to set it to:
<blat_bin>/opt/bin/blat</blat_bin>
<tmp_dir>ENTER_PATH_FOR_TEMPORARY_DATA</tmp_dir>
- For this instance, we need to set it to:
<tmp_dir>/data/dataHome/WebApollo2/Pyu/Blat/tmp</tmp_dir>
<database>ENTER_PATH_TO_BLAT_DATABASE</database>
- For this instance, we need to set it to:
<database>/data/dataHome/WebApollo2/Pyu/Blat/Pyu.2bit</database>
<blat_options>ENTER_ANY_BLAT_OPTIONS</blat_options>
- For this instance, we need to set it to:
<blat_options>-minScore=100 -minIdentity=60</blat_options>
Restart Tomcat
- The WebApollo instance should be set up now.
- Tomcat will need to be restarted for WebApollo to display properly.
sudo service tomcat7 restart
View your WebApollo instance
- You may view your instance by pointing your browser to
http://YOUR _HOST:8080/WebApollo2
- To view the site in JBrowse mode use this link format:
http://YOUR _HOST:8080/WebApollo2/jbrowse
Note on track styling
There are several pre-defined track styles included with the WebApollo release. If you'd like to use an included style, replace the subfeature section with the style name:
whatever-80pct green-80pct blue-80pct purple-80pct springgreen-80pct blueviolet-80pct mediumpurple-80pct orange-80pct darkorange-60pct
For example, to style a match type track with light green, adjust the load command like this:
--subfeatureClasses "{\"match_part\": \"darkblue-80pct\"}"
Becomes:
--subfeatureClasses "{\"match_part\": \"springgreen-80pct\"}"
These styles are located in the custom_track_styles.css file:
jbrowse/plugins/WebApollo2/css/custom_track_styles.css
You can also edit the styles after loading. The information on track styles are located in
jbrowse/data/trackList.json