Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
Rodolfo, Please keep the thread on the mailing list by using the "Reply all" option. You should now be able to go to the manage repository page, select the tool dependency, then select 'Manage tool dependencies' from the repository actions dropdown and reinstall the blast+ tool dependency. --Dave B. On 8/5/13 14:03:14.000, Rodolfo Aramayo wrote:
Dear Dave,
Answers below...
On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier <dave@bx.psu.edu> 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
fd4113962c32+ (stable)
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?
This is correct
We further understand that the repository is stuck in the 'installing' state.
YES and in the "Manage installed tool shed repositories" says now (after having to restart Galaxy for another reason):
"Installed, Missing tool dependencies"
What options are available from the popup menu next to the
ncbi_blast_plus repository on the manage installed repositories page?
If I click on the little arrow, it says:
Get updates Deactivate or uninstall
'Deactivate or uninstall' is available, can you try uninstalling again, and see if that functions correctly?
It worked!
Before I was not able to do it as I was getting an ugly galaxy error page But now it did uninstall and removed and was able to clone correctly. However, the directory:
./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/
is empty!
Should I repopulate it with the one I have in my backup??
Thanks
--Rodolfo
--Dave B.
On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote:
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Dave, See below.... On Mon, Aug 5, 2013 at 1:55 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Rodolfo,
Please keep the thread on the mailing list by using the "Reply all" option.
Apologies
You should now be able to go to the manage repository page, select the tool dependency, then select 'Manage tool dependencies' from the repository actions dropdown and reinstall the blast+ tool dependency.
--Dave B.
I did and it worked well it installed Blast 2.2.26+ However there are two problems: 1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'" The name, Version and Type display correct values. However the 'Installation status' shows no text 2. When I run the same blast job I was able to run before (using Blast+ 2.2.28+...that I installed) I get the following: error An error occurred with this dataset: blastn: 2.2.26+ Package: blast 2.2.26, build Aug 5 2013 14:01:30 Fatal error: Exit code 255 () Error: NCBI C++ Exception: "/usr/local/galaxy/galaxy-dist/database/tmp/tmpyhSi2d/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: Obviously it is the installed Blast that is at fault in here Thanks --R
On 8/5/13 14:03:14.000, Rodolfo Aramayo wrote:
Dear Dave,
Answers below...
On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier <dave@bx.psu.edu> 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
fd4113962c32+ (stable)
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?
This is correct
We further understand that the repository is stuck in the 'installing' state.
YES and in the "Manage installed tool shed repositories" says now (after having to restart Galaxy for another reason):
"Installed, Missing tool dependencies"
What options are available from the popup menu next to the
ncbi_blast_plus repository on the manage installed repositories page?
If I click on the little arrow, it says:
Get updates Deactivate or uninstall
'Deactivate or uninstall' is available, can you try uninstalling again, and see if that functions correctly?
It worked!
Before I was not able to do it as I was getting an ugly galaxy error page But now it did uninstall and removed and was able to clone correctly. However, the directory:
./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/
is empty!
Should I repopulate it with the one I have in my backup??
Thanks
--Rodolfo
--Dave B.
On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote:
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Rodolfo, --Dave B. On 8/5/13 15:50:46.000, Rodolfo Aramayo wrote:
Dave,
See below....
On Mon, Aug 5, 2013 at 1:55 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Rodolfo,
Please keep the thread on the mailing list by using the "Reply all" option.
Apologies
You should now be able to go to the manage repository page, select the tool dependency, then select 'Manage tool dependencies' from the repository actions dropdown and reinstall the blast+ tool dependency.
--Dave B.
I did and it worked well it installed Blast 2.2.26+
However there are two problems:
1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'" The name, Version and Type display correct values. However the 'Installation status' shows no text
2. When I run the same blast job I was able to run before (using Blast+ 2.2.28+...that I installed) I get the following:
error An error occurred with this dataset: blastn: 2.2.26+ Package: blast 2.2.26, build Aug 5 2013 14:01:30 Fatal error: Exit code 255 () Error: NCBI C++ Exception: "/usr/local/galaxy/galaxy-dist/database/tmp/tmpyhSi2d/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical:
Obviously it is the installed Blast that is at fault in here
Did the blast+ tool dependency compile without errors? You should be able to see any errors by clicking on the installed tool dependency, then expanding the blast+ folder and clicking on INSTALLATION.log
Thanks
--R
On 8/5/13 14:03:14.000, Rodolfo Aramayo wrote:
Dear Dave,
Answers below...
On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier <dave@bx.psu.edu> 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
fd4113962c32+ (stable)
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?
This is correct
We further understand that the repository is stuck in the 'installing' state.
YES and in the "Manage installed tool shed repositories" says now (after having to restart Galaxy for another reason):
"Installed, Missing tool dependencies"
What options are available from the popup menu next to the
ncbi_blast_plus repository on the manage installed repositories page?
If I click on the little arrow, it says:
Get updates Deactivate or uninstall
'Deactivate or uninstall' is available, can you try uninstalling again, and see if that functions correctly?
It worked!
Before I was not able to do it as I was getting an ugly galaxy error page But now it did uninstall and removed and was able to clone correctly. However, the directory:
./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/
is empty!
Should I repopulate it with the one I have in my backup??
Thanks
--Rodolfo
--Dave B.
On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote:
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Dave, It did contain errors as reported by tailing the last part of the INSTALLATION.log Thanks --Rodolfo make[4]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/blastdb' Updating dependency information for /usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/blastdb/blastdbcp.cpp. make[4]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/blastdb' make[4]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/blastdb' /usr/bin/g++ -c -Wall -Wno-format-y2k -g -fPIC -D_DEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DNCBI_WITHOUT_MT -I/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/inc -I/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/include /usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/blastdb/blastdbcp.cpp -o blastdbcp.o /usr/bin/g++ -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu -Wl,--enable-new-dtags -g -Wl,-E blastdbcp.o -Wl,-rpath,/usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/lib -Wl,-rpath-link,/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/lib -L/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/lib -lblastinput -lncbi_xloader_blastdb -lncbi_xloader_blastdb_rmt -lxblastformat -lalign_format -ltaxon1 -lblastdb_format -lgene_info -lxalnmgr -lblastxml -lxcgi -lxhtml -lwritedb -lxblast -lxalgoblastdbindex -lcomposition_adjustment -lxalgodustmask -lxalgowinmask -lseqmasks_io -lseqdb -lblast_services -lxobjutil -lxobjread -lcreaders -lxnetblastcli -lxnetblast -lblastdb -lscoremat -ltables -lxalnmgr -lncbi_xloader_genbank -lncbi_xreader_id1 -lncbi_xreader_id2 -lncbi_xreader_cache -lxconnext -lxconnect -ldbapi_driver -lncbi_xreader -lid1 -lid2 -lseqsplit -lxcompress -lxobjmgr -lgenome_collection -lseqset -lseqedit -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -lxconnext -lxser -lxcgi -lxhtml -lxconnect -lxutil -lxncbi -lz -lbz2 -ldl -lnsl -lrt -lm -o blastdbcp /bin/bash /usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/scripts/common/impl/if_diff.sh ln -f blastdbcp /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/bin ln -f blastdbcp /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/bin/blastdbcp make[4]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/blastdb' make -f /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.app.tmpl srcdir=/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/blastdb TMPL=makeprofiledb -w all make[4]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/blastdb' Updating dependency information for /usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/blastdb/makeprofiledb.cpp. make[4]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/blastdb' make[4]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/blastdb' /usr/bin/g++ -c -Wall -Wno-format-y2k -g -fPIC -D_DEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DNCBI_WITHOUT_MT -I/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/inc -I/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/include /usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/blastdb/makeprofiledb.cpp -o makeprofiledb.o /usr/bin/g++ -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu -Wl,--enable-new-dtags -g -Wl,-E makeprofiledb.o -Wl,-rpath,/usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/lib -Wl,-rpath-link,/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/lib -L/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/lib -lblastinput-static -lncbi_xloader_blastdb-static -lncbi_xloader_blastdb_rmt-static -lxblastformat-static -lalign_format-static -ltaxon1-static -lblastdb_format-static -lgene_info-static -lxalnmgr-static -lblastxml-static -lxcgi-static -lxhtml-static -lwritedb-static -lxblast-static -lxalgoblastdbindex-static -lcomposition_adjustment-static -lxalgodustmask-static -lxalgowinmask-static -lseqmasks_io-static -lseqdb-static -lblast_services-static -lxobjutil-static -lxobjread-static -lcreaders-static -lxnetblastcli-static -lxnetblast-static -lblastdb-static -lscoremat-static -ltables-static -lxalnmgr-static -lncbi_xloader_genbank-static -lncbi_xreader_id1-static -lncbi_xreader_id2-static -lncbi_xreader_cache-static -lxconnext-static -lxconnect-static -ldbapi_driver-static -lncbi_xreader-static -lid1-static -lid2-static -lseqsplit-static -lxcompress-static -lxobjmgr-static -lgenome_collection-static -lseqset-static -lseqedit-static -lseq-static -lseqcode-static -lsequtil-static -lpub-static -lmedline-static -lbiblio-static -lgeneral-static -lxser-static -lxutil-static -lxncbi-static -lz -lbz2 -ldl -lnsl -lrt -lm -o makeprofiledb /bin/bash /usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/scripts/common/impl/if_diff.sh ln -f makeprofiledb /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/bin ln -f makeprofiledb /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/bin/makeprofiledb make[4]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/blastdb' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/blastdb' make -C agpconvert -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/agpconvert' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/agpconvert' make -C id2_fetch -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/id2_fetch' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/id2_fetch' make -C agp_validate -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/agp_validate' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/agp_validate' make -C objextract -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/objextract' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/objextract' make -C lds_indexer -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/lds_indexer' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/lds_indexer' make -C bdb_env_keeper -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/bdb_env_keeper' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/bdb_env_keeper' make -C nw_aligner -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/nw_aligner' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/nw_aligner' make -C speedtest -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/speedtest' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/speedtest' make -C idmapper -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/idmapper' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/idmapper' make -C formatguess -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/formatguess' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/formatguess' make -C multireader -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/multireader' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/multireader' make -C read_blast_result -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/read_blast_result' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/read_blast_result' make -C splign -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/splign' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/splign' make -C hfilter -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/hfilter' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/hfilter' make -C annotwriter -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/annotwriter' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/annotwriter' make -C compart -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/compart' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/compart' make -C streamtest -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/streamtest' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/streamtest' NCBI_BUT_EXPENDABLE=' (but expendable)' make -C split_cache -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/split_cache' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/split_cache' NCBI_BUT_EXPENDABLE=' (but expendable)' make -C wig2table -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/wig2table' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/wig2table' NCBI_BUT_EXPENDABLE=' (but expendable)' make -C netcache -w all_r || exit 5 make[3]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/netcache' make[3]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app/netcache' make[2]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/app' make -C sample -w all_r || exit 5 make[2]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/sample' make[2]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/sample' make -C internal -w all_r || exit 5 make[2]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/internal' make[2]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/internal' make[1]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build' if test -f /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/bin/gbench; then \ make install-gbench; \ else \ make install-toolkit; \ fi make[1]: Entering directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++' /bin/rm -rf /usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/include/ncbi-tools++ /usr/local/bin/install -c -d /usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin /usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/lib /usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/include/ncbi-tools++ /usr/local/bin/install -c /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/bin/* /usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin /usr/local/bin/install -c -m 644 /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/lib/* /usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/lib cd /usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/include && find * -name CVS -prune -o -print |\ cpio -pd /usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/include/ncbi-tools++ /usr/local/bin/install -c -m 644 /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/inc/* /usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/include/ncbi-tools++ make[1]: Leaving directory `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++' ############################################# ############################################# cd c++ && ./configure --prefix=/usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a && make && make install STDERR configure: WARNING: Untested Boost version; may prove incompatible. configure: WARNING: If so, please re-run this script with the flag --without-boost. make[1]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/db/Makefile.in] Error 1 (ignored) make[1]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/db/Makefile.in] Error 1 (ignored) make[1]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/ctools/Makefile.in] Error 1 (ignored) make[1]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/ctools/Makefile.in] Error 1 (ignored) make[1]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/misc/Makefile.in] Error 1 (ignored) make[1]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/misc/Makefile.in] Error 1 (ignored) make[1]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/gui/Makefile.in] Error 1 (ignored) make[1]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/gui/Makefile.in] Error 1 (ignored) make[1]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/sample/Makefile.in] Error 1 (ignored) make[1]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/sample/Makefile.in] Error 1 (ignored) make[1]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/internal/Makefile.in] Error 1 (ignored) make[1]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/internal/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/corelib/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/corelib/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/util/image/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/util/image/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/util/qparse/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/util/qparse/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/util/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/util/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/util/demo/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/util/demo/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/util/tables/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/util/tables/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/util/bitset/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/util/bitset/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/util/bitset/demo/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/util/bitset/demo/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/connect/services/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/connect/services/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/connect/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/connect/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/connect/daemons/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/connect/daemons/Makefile.in] Error 1 (ignored) awk: cmd. line:1: fatal: cannot open file `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.flat' for reading (No such file or directory) WARNING: couldn't find connect/connect in /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.flat awk: cmd. line:1: fatal: cannot open file `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.flat' for reading (No such file or directory) WARNING: couldn't find connect/xconnect in /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.flat awk: cmd. line:1: fatal: cannot open file `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.flat' for reading (No such file or directory) WARNING: couldn't find connect/xxconnect in /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.flat make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/connect/ext/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/connect/ext/test/Makefile.in] Error 1 (ignored) awk: cmd. line:1: fatal: cannot open file `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.flat' for reading (No such file or directory) WARNING: couldn't find connect/ext/connext in /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.flat awk: cmd. line:1: fatal: cannot open file `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.flat' for reading (No such file or directory) WARNING: couldn't find connect/ext/xconnext in /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.flat make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/cgi/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/cgi/test/Makefile.in] Error 1 (ignored) awk: cmd. line:1: fatal: cannot open file `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.flat' for reading (No such file or directory) WARNING: couldn't find cgi/cgi in /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.flat awk: cmd. line:1: fatal: cannot open file `/data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.flat' for reading (No such file or directory) WARNING: couldn't find cgi/fcgi in /data/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/GCC460-Debug64/build/Makefile.flat make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/html/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/html/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/html/demo/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/html/demo/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/serial/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/serial/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/serial/soap/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/serial/soap/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/simple/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/simple/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/lang_bind/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/lang_bind/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/driver/util/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/driver/util/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/driver/ctlib/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/driver/ctlib/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/driver/ftds64/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/driver/ftds64/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/driver/dblib/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/driver/dblib/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/driver/mysql/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/driver/mysql/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/driver/samples/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/driver/samples/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/cache/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/cache/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/cache/admintool/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/dbapi/cache/admintool/Makefile.in] Error 1 (ignored) make[4]: *** [all] Error 2 make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objects/general/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objects/general/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objects/general/unit_test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objects/general/unit_test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objects/seq/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objects/seq/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objects/seq/unit_test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objects/seq/unit_test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objects/id1/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objects/id1/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objects/entrez2/demo/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objects/entrez2/demo/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objects/ncbimime/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objects/ncbimime/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objmgr/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objmgr/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objmgr/util/unit_test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objmgr/util/unit_test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/lds/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/lds/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/lds2/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/lds2/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/cddalignview/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/cddalignview/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/manip/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/manip/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/validator/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/validator/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/asniotest/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/asniotest/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/align/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/align/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/edit/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/edit/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/writers/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/writers/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/eutils/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/eutils/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/snputil/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/snputil/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/readers/app/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/readers/app/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/readers/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/readers/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/readers/unit_test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/readers/unit_test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/blast/gene_info_writer/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/blast/gene_info_writer/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/data_loaders/lds/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/data_loaders/lds/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/data_loaders/lds2/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/data_loaders/lds2/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/data_loaders/cdd/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/data_loaders/cdd/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/data_loaders/trace/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/data_loaders/trace/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/data_loaders/patcher/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/data_loaders/patcher/Makefile.in] Error 1 (ignored) make[4]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/data_loaders/genbank/test/Makefile.in] Error 1 (ignored) make[4]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/data_loaders/genbank/test/Makefile.in] Error 1 (ignored) make[4]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/data_loaders/blastdb/unit_test/Makefile.in] Error 1 (ignored) make[4]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/data_loaders/blastdb/unit_test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/alnmgr/demo/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/alnmgr/demo/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/cleanup/test/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/objtools/cleanup/test/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/sequence/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/sequence/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/align/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/align/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/structure/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/structure/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/ms/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/ms/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/gnomon/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/gnomon/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/tree/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/tree/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/phy_tree/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/phy_tree/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/seqqa/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/seqqa/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/cobalt/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/cobalt/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/text/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/text/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/volume_merge/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/volume_merge/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/blast/dbindex_search/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/blast/dbindex_search/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/blast/gumbel_params/Makefile.in] Error 1 (ignored) make[3]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/blast/gumbel_params/Makefile.in] Error 1 (ignored) make[4]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/blast/blastinput/demo/Makefile.in] Error 1 (ignored) make[4]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/algo/blast/blastinput/demo/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/asn2asn/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/asn2asn/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/asn2fasta/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/asn2fasta/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/asn2flat/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/asn2flat/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/asnval/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/asnval/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/id1_fetch/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/id1_fetch/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/convert_seq/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/convert_seq/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/nmer_repeats/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/nmer_repeats/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/objmgr/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/objmgr/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/gi2taxid/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/gi2taxid/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/netschedule/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/netschedule/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/grid/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/grid/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/agpconvert/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/agpconvert/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/id2_fetch/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/id2_fetch/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/agp_validate/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/agp_validate/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/objextract/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/objextract/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/lds_indexer/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/lds_indexer/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/bdb_env_keeper/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/bdb_env_keeper/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/nw_aligner/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/nw_aligner/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/speedtest/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/speedtest/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/idmapper/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/idmapper/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/formatguess/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/formatguess/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/multireader/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/multireader/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/read_blast_result/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/read_blast_result/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/splign/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/splign/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/hfilter/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/hfilter/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/annotwriter/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/annotwriter/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/compart/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/compart/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/streamtest/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/streamtest/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/split_cache/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/split_cache/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/wig2table/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/wig2table/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/netcache/Makefile.in] Error 1 (ignored) make[2]: [/usr/local/galaxy/galaxy-dist/database/tmp/tmp4sARKY/ncbi-blast-2.2.26+-src/c++/src/app/netcache/Makefile.in] Error 1 (ignored) 44024 blocks ############################################# ############################################# echo 'PATH=/usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin:$PATH; export PATH' > '/usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/env.sh';chmod +x '/usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/env.sh' STDOUT ############################################# ############################################# echo 'PATH=/usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin:$PATH; export PATH' > '/usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/env.sh';chmod +x '/usr/local/galaxy/bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/env.sh' STDERR ############################################# On Tue, Aug 6, 2013 at 8:16 AM, Dave Bouvier <dave@bx.psu.edu> wrote:
Rodolfo,
--Dave B.
On 8/5/13 15:50:46.000, Rodolfo Aramayo wrote:
Dave,
See below....
On Mon, Aug 5, 2013 at 1:55 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Rodolfo,
Please keep the thread on the mailing list by using the "Reply all" option.
Apologies
You should now be able to go to the manage repository page, select the tool dependency, then select 'Manage tool dependencies' from the repository actions dropdown and reinstall the blast+ tool dependency.
--Dave B.
I did and it worked well it installed Blast 2.2.26+
However there are two problems:
1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'" The name, Version and Type display correct values. However the 'Installation status' shows no text
2. When I run the same blast job I was able to run before (using Blast+ 2.2.28+...that I installed) I get the following:
error An error occurred with this dataset: blastn: 2.2.26+ Package: blast 2.2.26, build Aug 5 2013 14:01:30 Fatal error: Exit code 255 () Error: NCBI C++ Exception:
"/usr/local/galaxy/galaxy-dist/database/tmp/tmpyhSi2d/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical:
Obviously it is the installed Blast that is at fault in here
Did the blast+ tool dependency compile without errors? You should be able to see any errors by clicking on the installed tool dependency, then expanding the blast+ folder and clicking on INSTALLATION.log
Thanks
--R
On 8/5/13 14:03:14.000, Rodolfo Aramayo wrote:
Dear Dave,
Answers below...
On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier <dave@bx.psu.edu> 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
fd4113962c32+ (stable)
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?
This is correct
We further understand that the repository is stuck in the 'installing' state.
YES and in the "Manage installed tool shed repositories" says now (after having to restart Galaxy for another reason):
"Installed, Missing tool dependencies"
What options are available from the popup menu next to the
ncbi_blast_plus repository on the manage installed repositories page?
If I click on the little arrow, it says:
Get updates Deactivate or uninstall
'Deactivate or uninstall' is available, can you try uninstalling again, and see if that functions correctly?
It worked!
Before I was not able to do it as I was getting an ugly galaxy error page But now it did uninstall and removed and was able to clone correctly. However, the directory:
./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/
is empty!
Should I repopulate it with the one I have in my backup??
Thanks
--Rodolfo
--Dave B.
On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote:
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
On Tue, Aug 6, 2013 at 5:30 PM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
Dave,
It did contain errors as reported by tailing the last part of the INSTALLATION.log
Thanks
--Rodolfo
Looks like your BOOST is too new for BLAST 2.2.26+ (which just recently became a problem on the Galaxy Tool Shed testing system as well). In the short term I'm hoping to update the Tool Shed repository to use the NCBI provided pre-compiled binaries. I'm in discussion with Galaxy's Dave Bouvier about how best to do that, perhaps with some relatively new functionality added to Galaxy. Next, updating the BLAST+ version (and the unit tests to match). I would suggest right now you manually install BLAST+ using the NCBI provided binaries. Peter
On Tue, Aug 6, 2013 at 11:41 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Aug 6, 2013 at 5:30 PM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
Dave,
It did contain errors as reported by tailing the last part of the INSTALLATION.log
Thanks
--Rodolfo
Looks like your BOOST is too new for BLAST 2.2.26+ (which just recently became a problem on the Galaxy Tool Shed testing system as well).
In the short term I'm hoping to update the Tool Shed repository to use the NCBI provided pre-compiled binaries. I'm in discussion with Galaxy's Dave Bouvier about how best to do that, perhaps with some relatively new functionality added to Galaxy. Next, updating the BLAST+ version (and the unit tests to match).
I would suggest right now you manually install BLAST+ using the NCBI provided binaries.
Peter
Boost is a funny thing Changes a lot A package compiled with one Boost version might fail to compile with a newer one. I have seen it a lot You either have to download Boost and link to the specific version you want before compiling your package or provide pre-compiled binaries The question I have is: How many Galaxy packages have Boos as a dependency for compilation? and if the answer is: a lot, then would it be smart for Galaxy to have a place where it can keep versions of these commonly-used libraries so that they can be linked by packages that need to be compiled 'in-situ' or would it be just more efficient to provide pre-compiled binaries? Something tells me that pre-compiled binaries might not take full advantage of the hardware they are and that compiling is better... So, should ToolShed installation require automatic download of a set of pre-defined commonly-used libraries? --Rodolfo
On Wed, Aug 7, 2013 at 3:41 AM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
On Tue, Aug 6, 2013 at 11:41 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Looks like your BOOST is too new for BLAST 2.2.26+ (which just recently became a problem on the Galaxy Tool Shed testing system as well).
In the short term I'm hoping to update the Tool Shed repository to use the NCBI provided pre-compiled binaries. I'm in discussion with Galaxy's Dave Bouvier about how best to do that, perhaps with some relatively new functionality added to Galaxy. Next, updating the BLAST+ version (and the unit tests to match).
I would suggest right now you manually install BLAST+ using the NCBI provided binaries.
Peter
Boost is a funny thing Changes a lot A package compiled with one Boost version might fail to compile with a newer one. I have seen it a lot You either have to download Boost and link to the specific version you want before compiling your package or provide pre-compiled binaries The question I have is: How many Galaxy packages have Boos as a dependency for compilation? and if the answer is: a lot, then would it be smart for Galaxy to have a place where it can keep versions of these commonly-used libraries so that they can be linked by packages that need to be compiled 'in-situ' or would it be just more efficient to provide pre-compiled binaries? Something tells me that pre-compiled binaries might not take full advantage of the hardware they are and that compiling is better... So, should ToolShed installation require automatic download of a set of pre-defined commonly-used libraries?
That's probably possible via a Tool Shed dependency, Bjoern has been working on this on the Test Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_boost_1_53 Now under a shared IUC account: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53 Peter
Hi Rodolfo,
On Tue, Aug 6, 2013 at 11:41 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Aug 6, 2013 at 5:30 PM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
Dave,
It did contain errors as reported by tailing the last part of the INSTALLATION.log
Thanks
--Rodolfo
Looks like your BOOST is too new for BLAST 2.2.26+ (which just recently became a problem on the Galaxy Tool Shed testing system as well).
In the short term I'm hoping to update the Tool Shed repository to use the NCBI provided pre-compiled binaries. I'm in discussion with Galaxy's Dave Bouvier about how best to do that, perhaps with some relatively new functionality added to Galaxy. Next, updating the BLAST+ version (and the unit tests to match).
I would suggest right now you manually install BLAST+ using the NCBI provided binaries.
Peter
Boost is a funny thing Changes a lot A package compiled with one Boost version might fail to compile with a newer one. I have seen it a lot You either have to download Boost and link to the specific version you want before compiling your package or provide pre-compiled binaries The question I have is: How many Galaxy packages have Boos as a dependency for compilation? and if the answer is: a lot, then would it be smart for Galaxy to have a place where it can keep versions of these commonly-used libraries so that they can be linked by packages that need to be compiled 'in-situ' or would it be just more efficient to provide pre-compiled binaries? Something tells me that pre-compiled binaries might not take full advantage of the hardware they are and that compiling is better... So, should ToolShed installation require automatic download of a set of pre-defined commonly-used libraries?
As Peter already mentioned, the plan is to link specific versions of a tool to one specific version of boost. boost will also be installed and compiled. We plan to have a orphan tool dependency for every boost version like that one: http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53 To see how it should work, please have a look at my RDKit repository: http://testtoolshed.g2.bx.psu.edu/view/bgruening/rdkit Regarding your concerns about performance limitations with pre-compiled binaries, you are probably right. But do not forget the installation and compilation happens on one cluster node and the other nodes may also be different. So even with compiled versions you are not guaranteed to take full advantages of your hardware. Cheers, Bjoern
--Rodolfo ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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Hello Rodolfo, The following issue is resolved in 10319:61de03c05cf6 - thank for reporting this. Greg Von Kuster On Aug 5, 2013, at 3:50 PM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
I did and it worked well it installed Blast 2.2.26+
However there are two problems:
1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'" The name, Version and Type display correct values. However the 'Installation status' shows no text
You are very welcome So...what happened?? Thanks --R On Tue, Aug 6, 2013 at 9:26 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Rodolfo,
The following issue is resolved in 10319:61de03c05cf6 - thank for reporting this.
Greg Von Kuster
On Aug 5, 2013, at 3:50 PM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
I did and it worked well it installed Blast 2.2.26+
However there are two problems:
1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'" The name, Version and Type display correct values. However the 'Installation status' shows no text
Hi Rodolfo, There was a bug with regard to displaying the Installation status of a tool dcependency installed into Galaxy along with a repository from the Tool Shed. I have corrected this bug in the mentioned change set, so if you upgrade your Galaxy code to the mentioned revision, the installation status will now be displayed. Greg Von Kuster On Aug 6, 2013, at 10:29 AM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
You are very welcome So...what happened?? Thanks
--R
On Tue, Aug 6, 2013 at 9:26 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Rodolfo,
The following issue is resolved in 10319:61de03c05cf6 - thank for reporting this.
Greg Von Kuster
On Aug 5, 2013, at 3:50 PM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
I did and it worked well it installed Blast 2.2.26+
However there are two problems:
1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'" The name, Version and Type display correct values. However the 'Installation status' shows no text
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participants (5)
-
Bjoern Gruening -
Dave Bouvier -
Greg Von Kuster -
Peter Cock -
Rodolfo Aramayo