Treatment of blast in 3.3.4

[del...@gmail.com]

First, thank you dev team for all of the hard work!

 

I successfully brought up a 3.1-SNAPSHOT app, and momentarily was able to bring up gd-ice-3.3.3 or 3.3.4, I forget which at this point.

 

I shut down tomcat6 and cleaned up a few things, and have not been able to bring up 3.3.3, 3.3.4, 3.3.5 since then. I had tomcat6 / Java issues, now resolved, thanks to Hector. Now upon startup I'm getting what appear to be blast-related errors in catalina.out. I have included my jbeir.properties file below that, can someone advise about the blast / jbeir.properties configuration?

 

I notice there are some blast bits in ice-linux-3.3.4.tar, I've tried putting them in tomcat's PATH, put them all in /usr/share/tomcat6/blast/bin, modified JBEIR.PROPERTIES to point to the new locations, etc., etc., etc. (the usual uninformed troubleshooting stuff), tried adding /usr/share/tomcat6/jbeiblast, and so on. I suppose I need to figure out how to properly install blast?

 

While I'm on the subject, what is the relationship of that distribution (ice-linux) and the various gd-ice-3.3.X-SNAPSHOT distributions?

 

thanks in advance!

Dan Lewis

 

Error from catalina.out:

 

INFO  - TableMetadata              - HHH000261: Table found: public.trace_sequence_alignments
INFO  - TableMetadata              - HHH000037: Columns: [subject_alignment, id, sequence_hash, strand, subject_start, score, modification_time, trace_sequence_id, query_end, query_start, query_alignment, subject_end]
INFO  - system                     - Application version: 3.3.0
INFO  - system                     - Checking blast database
INFO  - system                     - Adding task
INFO  - system                     - Running blast rebuild task
ERROR - system                     - org.jbei.ice.lib.search.blast.BlastException: java.nio.file.AccessDeniedException: /usr/share/tomcat6/blast
        at org.jbei.ice.lib.search.blast.Blast.rebuildDatabase(Blast.java:113)
        at org.jbei.ice.lib.search.blast.RebuildBlastIndexTask.execute(RebuildBlastIndexTask.java:24)
        at org.jbei.ice.lib.executor.TaskHandler.run(TaskHandler.java:22)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:722)
Caused by: java.nio.file.AccessDeniedException: /usr/share/tomcat6/blast
        at sun.nio.fs.UnixException.translateToIOException(UnixException.java:84)
        at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
        at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
        at sun.nio.fs.UnixFileSystemProvider.createDirectory(UnixFileSystemProvider.java:382)
        at java.nio.file.Files.createDirectory(Files.java:628)
        at java.nio.file.Files.createAndCheckIsDirectory(Files.java:732)
        at java.nio.file.Files.createDirectories(Files.java:718)
        at org.jbei.ice.lib.search.blast.Blast.rebuildDatabase(Blast.java:94)
        ... 5 more

 

 

JBEIR.PROPERTIES

 

TEMPORARY_DIRECTORY=/tmp
DATA_DIRECTORY=/tmp
ATTACHMENTS_DIRECTORY=/tmp/attachments
TRACE_FILES_DIRECTORY=/tmp/traces
BLAST_DIRECTORY=/tmp/blast
# Random Salt. Change for your site
SITE_SECRET=Secret Sauce
SECRET_KEY=thisisaplaceholderformysecretkey
COOKIE_NAME=gd-ice
#email of user to be notified of pending bulk uploads
#leave empty if no notification is desired
BULK_UPLOAD_APPROVER_EMAIL=
ADMIN_EMAIL=friend...@hms.harvard.edu
SMTP_HOST=
ERROR_EMAIL_EXCEPTION_PREFIX=[ERROR]
SEND_EMAIL_ON_ERRORS=YES
PROJECT_NAME=JBEI Registry
URI_PREFIX=http://registry.jbei.org
PART_NUMBER_PREFIX=TEST
PART_NUMBER_DIGITAL_SUFFIX=000001
PART_NUMBER_DELIMITER=_
WIKILINK_PREFIX=jbei
# 300000ms = 5 minutes"
BLAST_BLASTALL=/usr/bin/blastall
BLAST_BL2SEQ=/usr/bin/bl2seq
BLAST_FORMATDB=/usr/bin/formatdb
BLAST_DATABASE_NAME=jbeiblast
# LocalBackend, NullAuthenticationBackend, LblLdapAuthentication are built-in
AUTHENTICATION_BACKEND=org.jbei.ice.lib.authentication.NullAuthenticationBackend
LDAP_SEARCH_URL=ldap://
LDAP_AUTHENTICATION_URL=ldaps://
LDAP_QUERY=
NEW_REGISTRATION_ALLOWED=yes
PASSWORD_CHANGE_ALLOWED=yes
PROFILE_EDIT_ALLOWED=yes

[Del0654]

By observing catalina.out and it's logged attempts to find blast, I discovered it wanted blast bits in /usr/share/tomcat6/blast and also blast-2.2.26. The app appears to ignore the blast settings in jbeir.properties. In addition, when I save new settings by using the app's Admin functions, I can't discover where the settings are saved.

 

What is the proper placement & treatment of jbeir.properties, and where does the app store new preferences, if not there?

 

TIA,

Dan Lewis

--
 
---
You received this message because you are subscribed to a topic in the Google Groups "gd-ice" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/gd-ice/1pSV3eh8FiQ/unsubscribe.
To unsubscribe from this group and all its topics, send an email to gd-ice+un...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

[Michal Galdzicki]

Hi Dan,

I'm not on the team. But I've asked a similar question before. 

jbeir.properties are ignored, deprecated in the newer versions.

The online properties are stored in the database.

If you find a solution could you post here,

-mike

--
 
---
You received this message because you are subscribed to the Google Groups "gd-ice" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gd-ice+un...@googlegroups.com.

[Hector Plahar]

As Mike mentioned, JBEIR.properties is deprecated. It is ignored for new installations. All the properties are now stored in the database and can be modified on the admin page. When signed in as an administrator you should see the "Admin" main link. Under the System Settings, you should see search settings. Modify blastall etc properties to point to the location of the installation.  A quick way to bundle blast is to download legacy blast (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/). Version 3.4 will have BLAST+ support.

ice-linux-3.3.4.tar is essentially gd-ice-3.3.4-SNAPSHOT bundled with tomcat. It is meant to provide a quick and convenient way for users to evaluate ICE on their local machines. 

Thanks,

Hector.

ADMIN_EMAIL=...@hms.harvard.edu