How to Uninstall NCBI_Blast_Plus from ToolShed
People, I successfully installed NCBI_Blast_Plus from the toolshed The tool, however, failed to work giving the following error: Fatal error: Exit code 255 () Error: NCBI C++ Exception: "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. I then tried uninstalling/reinstalling the tool However I now get an eternal 'installing' grey message and when I click 'manage the repo' I get: ######### URL: http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990... File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 561 in manage_repository repository = suc.get_installed_tool_shed_repository( trans, repository_id ) File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py', line 515 in get_installed_tool_shed_repository return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b' ######### How can I totally uninstall and re-install this tool? Thanks
On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
I've seen that kind of error from NCBI BLAST+ before - do you know which of the BLAST tools was this, and what the query was?
I then tried uninstalling/reinstalling the tool
I doubt that will make any difference at all - this null pointer exception is not a problem from Galaxy.
You seem to have found a bug in the Tool Shed, so thank you for reporting this. Peter
On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
The repo was: repos/devteam/ncbi_blast_plus/9dabbfd73c8a/ncbi_blast_plus The query was: Output from velvetoptimiser /repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser
You are welcome But any ideas on how to properly uninstall and re-install the tool?? Thanks --R
Peter
On Thu, Aug 1, 2013 at 1:41 PM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
OK, so this was a nucleotide FASTA file from an assembly, right? What were you searching with BLAST? e.g. BLASTN against NT, BLASTX against NR, etc.
Hopefully Greg from the Galaxy team will be able to help with this. Peter
On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Yes
What were you searching with BLAST? e.g. BLASTN against NT, BLASTX against NR, etc.
Search was blastn, task megablast of the assembly as query against an in-house made (and installed into galaxy) of a blastn database for Chromosomes 1 to 7 of Neurospora crassa Database was produced with: makeblastdb -in Ncrassa_wt_Chr01.Chr07_v12 -dbtype nucl -title Ncrassa_wt_Chr01.Chr07_v12 -parse_seqids -hash_index and "installed" into the "blastdb.loc" file as required Thanks
On Thu, Aug 1, 2013 at 2:47 PM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
Can you run this blastn search 'by hand' at the terminal? Does that crash too? The error sounds very similar to this report which turned out to be due to a corrupted BLAST database - so also try recreating your DB: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644962 Peter
Dear Peter, APOLOGIES for the delayed response Please see below for details...... On Thu, Aug 1, 2013 at 8:51 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Yes, yes and no
Does that crash too?
No and I do not know Please let me explain. I have set up the user galaxy account such that it has access to a directory called 'bioinfosoft' where all bioinformatics-related software is installed, including Blast+ Galaxy has 'access' to this directory and there I have compiled Blast+ 2.2.28+ Now, when I installed Blast+ via the toolshed, the toolshed Blast+ package did download and install what I believe it was the 2.2.26+ version of Blast+? If I recall correctly, I got an error message that went away while the Blast+ package was being compiled by the toolshed The errors I got running Blast did all occur when using that particular version of Blast+ (2.2.26) I then removed or uninstalled the packaged and tried to re-install again, but, as I said, it hanged there forever, installing... To my surprise when I re-run the jobs, they all worked well. This is, Blast worked like a charm BUT it did because it is NOT using the Blast packaged that was installed by the toolshed but the Blast package I compiled myself (2.2.28+) (SEE LOG AT END OF THIS MESSAGE...) Comparing the directory of galaxy with those of my backups I can see that the packaged Blast 2.2.26+ that was installed by the toolshed in the directory: ./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/ is no longer there.. The directory: ./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/ is present but it is empty Therefore to answer your questions:
Can you run this blastn search 'by hand' at the terminal?
Yes, I can but I would be using a different version of Blast+
Does that crash too?
No, because I would be using a different version of Blast+
Regarding this last comment..basically a corrupt database is not the problem in this case as demonstrated by the fact that I can run Blast on those databases Having said that, yes I have observed that depending on how one runs the makeblastdb command and depending on the type of fasta files used, you can end up with corrupt output. Some identifiers and symbols present in the fasta ID can interfere with makeblastdb (especially some produced by the JGI) In summary, yes Blast+ is working but because is not using the compiled Blast+ binaries installed by the toolshed package The problem I have is that I would like to be able to properly uninstall and re-install the Blast+ toolsheed so that things work as they were originally supossed to On the other hand, if you guys upgrade the package, this might be a non-issue as the toolshed would just simply generate new directories... Last, I noticed the command used in the compilation is different from the one I normally use The command I use is: tar -xzvf ncbi-blast-2.2.28+-src.tar.gz cd ncbi-blast-2.2.28+-src/c++ ./configure --prefix=/usr/local/galaxy/bioinfosoft/blast-2.2.28+ --with-64 --with-bincopy --with-mt --without-debug --with-static | tee c.log make | tee m.log make check make install Many Thanks --Rodolfo
Peter
LOG: galaxy.jobs.handler INFO 2013-08-05 12:11:30,841 (2405) Job dispatched galaxy.tools DEBUG 2013-08-05 12:11:31,018 Building dependency shell command for dependency 'blastn' galaxy.tools WARNING 2013-08-05 12:11:31,018 Failed to resolve dependency on 'blastn', ignoring galaxy.tools DEBUG 2013-08-05 12:11:31,018 Building dependency shell command for dependency 'blast+' galaxy.tools WARNING 2013-08-05 12:11:31,018 Failed to resolve dependency on 'blast+', ignoring galaxy.jobs.runners.local DEBUG 2013-08-05 12:11:31,099 (2405) executing: blastn -version &> /usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_2405; blastn -query "/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2897.dat" -db "/data/db/fungidb/Ncrassa_OR74A/blastplus_db/Ncrassa_wt_Chr01.Chr07.+ChrM.+rDNA_v12" -task megablast -evalue 0.001 -out "/usr/local/galaxy/galaxy-dist/database/files/003/dataset_3596.dat" -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -num_threads 8 galaxy.jobs DEBUG 2013-08-05 12:11:31,152 (2405) Persisting job destination (destination id: local) galaxy.jobs.runners.local DEBUG 2013-08-05 12:11:32,230 execution finished: blastn -version &> /usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_2405; blastn -query "/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2897.dat" -db "/data/db/fungidb/Ncrassa_OR74A/blastplus_db/Ncrassa_wt_Chr01.Chr07.+ChrM.+rDNA_v12" -task megablast -evalue 0.001 -out "/usr/local/galaxy/galaxy-dist/database/files/003/dataset_3596.dat" -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -num_threads 8 galaxy.jobs.runners DEBUG 2013-08-05 12:11:32,324 executing external set_meta script for job 2405: /usr/local/galaxy/galaxy-dist/set_metadata.sh ./database/files /usr/local/galaxy/galaxy-dist/database/job_working_directory/002/2405 . /usr/local/galaxy/galaxy-dist/universe_wsgi.ini /usr/local/galaxy/galaxy-dist/database/tmp/tmp7F7qqE /usr/local/galaxy/galaxy-dist/database/job_working_directory/002/2405/galaxy.json /usr/local/galaxy/galaxy-dist/database/job_working_directory/002/2405/metadata_in_HistoryDatasetAssociation_4245_qhcDd5,/usr/local/galaxy/galaxy-dist/database/job_working_directory/002/2405/metadata_kwds_HistoryDatasetAssociation_4245_pKXnUR,/usr/local/galaxy/galaxy-dist/database/job_working_directory/002/2405/metadata_out_HistoryDatasetAssociation_4245_jSXP0f,/usr/local/galaxy/galaxy-dist/database/job_working_directory/002/2405/metadata_results_HistoryDatasetAssociation_4245_WzHo1J,,/usr/local/ galaxy/galaxy-dist/database/job_working_directory/002/2405/metadata_override_HistoryDatasetAssociation_4245_OBr8F0 galaxy.jobs.runners DEBUG 2013-08-05 12:11:33,882 execution of external set_meta for job 2405 finished
On Mon, Aug 5, 2013 at 6:50 PM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
OK, so there are still issues with the Tool Shed itself, but the BLAST issue seems to have gone away when using a newer version (compiled). I'm working on using the NCBI provided binaries if possible, but updating the Galaxy BLAST+ bundle to a newer version of the underlying BLAST tools is planned. Thanks, Peter
The statement "there are still issues with the Tool Shed itself" is not confirmed, correct? I believe we're still waiting on the response to Dave's initial response below. Or did I miss it??? On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier <dave@bx.psu.edu> wrote:
On Aug 5, 2013, at 2:35 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Rodolfo, In order to simplify tracking down this issue, could you provide the changeset revision of Galaxy that is running on tamu.edu? To retrieve the revision, execute the following command in your galaxy root directory: hg id To clarify, our understanding is that you installed the ncbi_blast_plus repository from the main tool shed, and it installed correctly. You then uninstalled the repository, and it also uninstalled properly. You then attempted to reinstall the repository, and encountered the error message cited in your email. Can you confirm the above? We further understand that the repository is stuck in the 'installing' state. What options are available from the popup menu next to the ncbi_blast_plus repository on the manage installed repositories page? If 'Deactivate or uninstall' is available, can you try uninstalling again, and see if that functions correctly? --Dave B. On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote:
Dave, Also, when I click on: "Get repository update" I get the following error: ########################################################## URL: http://galaxy.tamu.edu/admin_toolshed/check_for_updates?id=ff08d6222f8e14990... File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 202 in check_for_updates repository = suc.get_installed_tool_shed_repository( trans, repository_id ) File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py', line 515 in get_installed_tool_shed_repository return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b' ########################################################## Thanks --R On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier <dave@bx.psu.edu> wrote:
Trying out a local instance of Galaxy. Small files can be uploaded with "browse.." but this works only for files under 2Gb. Is there a folder in a local copy of galaxy-dist where I can copy a large file and have it show up in the Get Data/Upload File/Files uploaded via FTP window so that I can properly get it into the local history? Copying it directly into the database seemed not to work, it didn't show up anywhere. Gerald
Hi Gerald Have you looked into 'Data Libraries'? http://wiki.galaxyproject.org/Admin/DataLibraries/Libraries http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles This will allow you to access the files without data duplication. Regards, Hans-Rudolf On 08/05/2013 08:48 PM, Gerald Bothe wrote:
participants (6)
-
Dave Bouvier -
Gerald Bothe -
Greg Von Kuster -
Hans-Rudolf Hotz -
Peter Cock -
Rodolfo Aramayo