[galaxy-dev] blast+ wrapper with remote searching
Hello all, The newly developed blast+ wrappers seem to be very useful, but it seems like they do not contain the function to blast against remote servers instead of installing the databases locally. Am I missing something there? I need to do a remote search for a sequence within galaxy instance so I can automate the process. Help is much appreciated. Thanks a lot, Nilaksha ___ 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/
Re: [galaxy-dev] blast+ wrapper with remote searching
On Wed, Mar 19, 2014 at 6:42 AM, Nilaksha Neththikumara nilakshafree...@gmail.com wrote: Hello all, The newly developed blast+ wrappers seem to be very useful, but it seems like they do not contain the function to blast against remote servers instead of installing the databases locally. Am I missing something there? I need to do a remote search for a sequence within galaxy instance so I can automate the process. Help is much appreciated. Thanks a lot, Nilaksha Hi Nilaksha, You are correct, the BLAST+ wrappers for Galaxy don't currently support the -remote option to connect to the NCBI over the internet to run the searches there - we've talked about this though, and I've filed an issue to track this in future: https://github.com/peterjc/galaxy_blast/issues/39 What do you mean by you need remote search for automation? You can download all the NCBI managed databases like NT/NR locally, so most tasks can be done without the -remote option. Peter P.S. The BLAST+ wrappers aren't 'newly developed', work started way back in 2011 ;) ___ 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/
Re: [galaxy-dev] Tool Testing Enhancements
On Tue, Mar 18, 2014 at 7:10 PM, John Chilton jmchil...@gmail.com wrote: Hi Peter, Thanks for the bug report. It looks like if requests is available to the framework these unicode errors go away (it doesn't have to fall back on my poor attempt to provide a similar interface). https://github.com/jmchilton/pico_galaxy/commit/e7d37f31951d8e729cfdbda0ca9085feb7f2da73 I'll create a Trello card and try to add an egg for this - other developers on the team have likewise said they would like a requests dependency available in the past so I doubt there will be objections. -John Great, I'll use the manual 'requests' install for TravisCI in the short term... P.S. It looks like the ftype changeset has already caught some errors (your sample_seqs tool only produces fasta outputs but some outputs are labelled as sff): https://travis-ci.org/jmchilton/pico_galaxy/jobs/21036295 Thanks - it was missing a change_format tag: https://github.com/peterjc/pico_galaxy/commit/a2bc5fe8866fc9587e04a9fd84df50e010cdd52b Peter ___ 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/
[galaxy-dev] Running a different command based on selection in the tool
Hi all, I am trying to write a tool that based on user criteria will run a different script. In the code below, If I select Use_Snapshot, I see the right interface but somehow galaxy tries to execute the #else part and look for “m” input parameter. The example I have seen in documentation is using the script with same name in both if and else and the number of input arguments is the same as well. Any suggestions/ideas why always #else part gets executed although right interface appears based on user selection. Thanks, Saba command #if $source.source_select==“Use_Snapshot cM-snapshot.sh $input $output #else cM.sh $m $b $ns $w $s $z $output #end if /command inputs conditional name=source param name=source_select type=select label=Specify the input option value=Use_SnapshotUse Snapshot/option option value=Set_ValuesSet Values/option /param when value=Use_Snapshot param name=input type=data format=dbm size=100 label=Input Snapshot/ sanitizer sanitize=False/ /when when value=Set_Values param name=m label=Omega_m h^2 type=float value=0.1279 min=0.120 max=0.155/ param name=b label=Omega_b h^2 type=float value=0.0232 min=0.0215 max=0.0235/ param name=ns label=n_s type=float value=0.8629 min=0.85 max=1.05/ param name=w label=wtype=float value=-1.184 min=-1.30 max=-0.70/ param name=s label=sigma_8 type=float value=0.6159 min=0.61 max=0.9/ param name=z label=ztype=float value=1.0 min=0.0 max=1.0/ sanitizer sanitize=False/ /when /conditional /inputs ___ 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/
[galaxy-dev] Running a different command based on selection in the tool
Hi all, I am trying to write a tool that based on user criteria will run a different script. In the code below, If I select Use_Snapshot, I see the right interface but somehow galaxy tries to execute the #else part and look for “m” input parameter. The example I have seen in documentation is using the script with same name in both if and else and the number of input arguments is the same as well. Any suggestions/ideas why always #else part gets executed although right interface appears based on user selection. Thanks, Saba command #if $source.source_select==“Use_Snapshot cM-snapshot.sh $input $output #else cM.sh $m $b $ns $w $s $z $output #end if /command inputs conditional name=source param name=source_select type=select label=Specify the input option value=Use_SnapshotUse Snapshot/option option value=Set_ValuesSet Values/option /param when value=Use_Snapshot param name=input type=data format=dbm size=100 label=Input Snapshot/ sanitizer sanitize=False/ /when when value=Set_Values param name=m label=Omega_m h^2 type=float value=0.1279 min=0.120 max=0.155/ param name=b label=Omega_b h^2 type=float value=0.0232 min=0.0215 max=0.0235/ param name=ns label=n_s type=float value=0.8629 min=0.85 max=1.05/ param name=w label=wtype=float value=-1.184 min=-1.30 max=-0.70/ param name=s label=sigma_8 type=float value=0.6159 min=0.61 max=0.9/ param name=z label=ztype=float value=1.0 min=0.0 max=1.0/ sanitizer sanitize=False/ /when /conditional /inputs___ 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/
[galaxy-dev] Bowtie2 and tophat2 data library set up
Hi, I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more. https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Can you direct me to the right page or send me the documents please? Thanks, Huayan ___ 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/
[galaxy-dev] migrate to postgresql
Hi all, I followed the instruction on https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer and managed to migrate to a postgresql on a Ubuntu machine. However when I tried on a CentOS 6.5, it failed.The steps are: 1. Create psql user galaxy: under psql prompt, a. CREATE USER galaxy WITH PASSWORD 'galaxy'; b. CREATE DATABASE galaxy; c. GRANT ALL PRIVILEGES ON DATABASE galaxy to galaxy; 2. test the created account: change authentication method to password in pg_hba.conf and the username/password works 3. add postgresql://galaxy:galaxy@localhost/galaxy to universal_wsgi.ini 4. sh run.sh gave me the error saying FATAL: Ident authentication failed for user galaxy 5. even I changed back to the default IDENT authentication for postgresql in pg_hba.conf, the same error message appeared. Could anyone help me to spot the error here? Best regards! Jun ___ 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/
Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
Hello Huayan, I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+cd=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao huayan...@gmail.com wrote: Hi, I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more. https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Can you direct me to the right page or send me the documents please? Thanks, Huayan ___ 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/ ___ 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/
Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
Hello again Huayan, the page got renamed and redirect was not in place. I have put it there and the new page has even more info on it! :) thank you for using Galaxy! Martin On Wed, Mar 19, 2014 at 10:18 PM, Martin Čech mar...@bx.psu.edu wrote: Hello Huayan, I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+cd=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao huayan...@gmail.com wrote: Hi, I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more. https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Can you direct me to the right page or send me the documents please? Thanks, Huayan ___ 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/ ___ 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/
Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
Thanks Martin! One more question, I want to install all the migrated tools from stage 9, that is NGS tools to my local galaxy. I tried but always got some problems. Do you have the instructions on wiki too? Thanks, Huayan On Thu, Mar 20, 2014 at 10:27 AM, Martin Čech mar...@bx.psu.edu wrote: Hello again Huayan, the page got renamed and redirect was not in place. I have put it there and the new page has even more info on it! :) thank you for using Galaxy! Martin On Wed, Mar 19, 2014 at 10:18 PM, Martin Čech mar...@bx.psu.edu wrote: Hello Huayan, I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+cd=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao huayan...@gmail.com wrote: Hi, I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more. https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Can you direct me to the right page or send me the documents please? Thanks, Huayan ___ 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/ ___ 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/
Re: [galaxy-dev] Running a different command based on selection in the tool
Hi Saba, there is a syntax error in the line of the #if. Please add : at the end and report whether the error still occurs. All the best, Jens Von: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Im Auftrag von Saba Sehrish Gesendet: Mittwoch, 19. März 2014 23:07 An: galaxy-dev@lists.bx.psu.edu Betreff: [galaxy-dev] Running a different command based on selection in the tool Hi all, I am trying to write a tool that based on user criteria will run a different script. In the code below, If I select Use_Snapshot, I see the right interface but somehow galaxy tries to execute the #else part and look for m input parameter. The example I have seen in documentation is using the script with same name in both if and else and the number of input arguments is the same as well. Any suggestions/ideas why always #else part gets executed although right interface appears based on user selection. Thanks, Saba command #if $source.source_select==Use_Snapshot cM-snapshot.sh $input $output #else cM.sh $m $b $ns $w $s $z $output #end if /command inputs conditional name=source param name=source_select type=select label=Specify the input option value=Use_SnapshotUse Snapshot/option option value=Set_ValuesSet Values/option /param when value=Use_Snapshot param name=input type=data format=dbm size=100 label=Input Snapshot/ sanitizer sanitize=False/ /when when value=Set_Values param name=m label=Omega_m h^2 type=float value=0.1279 min=0.120 max=0.155/ param name=b label=Omega_b h^2 type=float value=0.0232 min=0.0215 max=0.0235/ param name=ns label=n_s type=float value=0.8629 min=0.85 max=1.05/ param name=w label=wtype=float value=-1.184 min=-1.30 max=-0.70/ param name=s label=sigma_8 type=float value=0.6159 min=0.61 max=0.9/ param name=z label=ztype=float value=1.0 min=0.0 max=1.0/ sanitizer sanitize=False/ /when /conditional /inputs ___ 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/
Re: [galaxy-dev] blast+ wrapper with remote searching
Thanks a lot for the information. :) I'm new to the field so get confused at times. I started downloading the NCBI databases locally, but I have two questions. 1) There is no proper updating process for the locally installed NCBI databases. (according to my knowledge) So it seems I have to re download the database totally if I need to get them updated. And those databases are almost always being updating. (.sigh) 2) After installing databases, is there a particular way to let galaxy know where are my databases located? So that they can be included in the drop down menu of the blast+ wrappers for me to select :) Thanks a lot in advance Nilaksha Neththikumara. On Wed, Mar 19, 2014 at 3:33 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wed, Mar 19, 2014 at 6:42 AM, Nilaksha Neththikumara nilakshafree...@gmail.com wrote: Hello all, The newly developed blast+ wrappers seem to be very useful, but it seems like they do not contain the function to blast against remote servers instead of installing the databases locally. Am I missing something there? I need to do a remote search for a sequence within galaxy instance so I can automate the process. Help is much appreciated. Thanks a lot, Nilaksha Hi Nilaksha, You are correct, the BLAST+ wrappers for Galaxy don't currently support the -remote option to connect to the NCBI over the internet to run the searches there - we've talked about this though, and I've filed an issue to track this in future: https://github.com/peterjc/galaxy_blast/issues/39 What do you mean by you need remote search for automation? You can download all the NCBI managed databases like NT/NR locally, so most tasks can be done without the -remote option. Peter P.S. The BLAST+ wrappers aren't 'newly developed', work started way back in 2011 ;) ___ 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/
Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
Hi Martin, Actually I want a NGS Toolbox Beta tool panel exactly like the usegalaxy.org. How can I achieve this? I found myself looking for the tools and put them to tool_conf.xml which is very tedious. Is there a better way to do it? Best, Huayan On Thu, Mar 20, 2014 at 11:43 AM, Huayan Gao huayan...@gmail.com wrote: Thanks Martin! One more question, I want to install all the migrated tools from stage 9, that is NGS tools to my local galaxy. I tried but always got some problems. Do you have the instructions on wiki too? Thanks, Huayan On Thu, Mar 20, 2014 at 10:27 AM, Martin Čech mar...@bx.psu.edu wrote: Hello again Huayan, the page got renamed and redirect was not in place. I have put it there and the new page has even more info on it! :) thank you for using Galaxy! Martin On Wed, Mar 19, 2014 at 10:18 PM, Martin Čech mar...@bx.psu.edu wrote: Hello Huayan, I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+cd=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao huayan...@gmail.com wrote: Hi, I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more. https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Can you direct me to the right page or send me the documents please? Thanks, Huayan ___ 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/ ___ 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/
