- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] samtools index tool
by Eleanor Morgan 22 May '15

22 May '15

Hi all, Excuse me for the newbie question. I am developing a local instance of galaxy to use primarily for teaching purposes. I would like to index bam files produced in galaxy in order to view them in IGV. I can't seem to find the samtools index tool in the toolshed. I can run samtools on the command line and generate indexes, but can find no way to add this functionality to the tool panel so that I can do it in Galaxy. I also can't find this functionality in the tool panel (under Samtools or BAM tools) on usegalaxy.org. Am I missing something? Do I need to write my own tool? Regards, Eleanor Eleanor Morgan Senior Scientific Officer | School of Biomedical Sciences | Faculty of Health Sciences Curtin University Tel | +61 8 9266 7516 Mob | +61 408 004 369 Fax | +61 8 9266 2342 Email | e.morgan(a)curtin.edu.au<mailto:e.morgan@curtin.edu.au> Web | biomed.curtin.edu.au [cid:ED62B336-732F-4D99-ABF8-AFACA1E1C7E3] Curtin University is a trademark of Curtin University of Technology. CRICOS Provider Code 00301J (WA), 02637B (NSW)

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connecting composite data elements to a display application
by Brian Haas 21 May '15

21 May '15

Greetings. I have composite data stored with extra files like so: galaxy/database/files/000/dataset_150.dat and galaxy/database/files/000/dataset_150_files and I'm trying to set up a display link that provides a URL that embeds links to the files stored in the /dataset_150_files/ directory. I've studied the documentation here: https://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Application… but can't quite figure out how to reference these extra data files. any help would be greatly appreciated. many thanks, ~brian -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

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Bug with boolean param (with truevalue)
by Christian Brenninkmeijer 21 May '15

21 May '15

Hi All, We have been trying to use a param with type boolean in a conditional. Because of the Case inconsistency between the when clause (lower case) and the command clause (Capitalized) we tried to use the truevalue options. For example (Full xml and code attached) <conditional name="bdg_options2"> <param name="bdg2" type="boolean" checked="false" truevalue="changed" falsevalue="unchanged" label="Boolean 2" /> <when value="changed"> .... </when> <when value="unchanged"> ... </when> </conditional> Unfortunately this showed up various bugs. 1. The value set by truevalue="..." works in the when but is lost in the <command> where it reverst back to True/False (Both in Galaxy and Planemo) 2. In Planemo you can change a param which defaults to True to False but you can not change a param that defaults to False to True -Works ok in Galaxy 3. In Planemo you can use the value set by falsevalue="xyz" to set the boolean param but ONLY to change a true to a false but not a false to a true. regards Christian Brenninkmeijer PS. If the attachments do not work I will repost with the full xml and code

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any working example of auth_conf.xml validating against openldap?
by Pablo Escobar 20 May '15

20 May '15

Hi, currently I am validating my users with openldap in apache. As in the new release of galaxy there is native support to validate againts ldap from galaxy I have upgraded to latest galaxy release and I am trying to configure auth_conf.xml but I cannot manage to get it working with my openldap. I see the provided example auth_conf.xml.sample is validating again active directory. Can anyone provide a working auth_conf.xml which is working with openldap so I can take it as reference? thanks in advance for any help. regards, Pablo.

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Adding BioPython as a dependency to Galaxy
by Eric Rasche 20 May '15

20 May '15

Howdy Devs, I'd like to see BioPython added as an egg. I mentioned this on IRC, but it sort of fell off. A couple of users spoke positively about having it as a dependency. Do any of the devs have further opinions on this? Can we add it? Depending on BioPython would provide us with a lot of utility in the datatype/datatype conversion area. I'm, personally, interested in adding/expanding all of the datatypes from SeqIO <https://github.com/biopython/biopython/tree/master/Bio/SeqIO> (e.g. EMBL/GenBank/etc) and AlignIO <https://github.com/biopython/biopython/tree/master/Bio/AlignIO> (Stockholm/clustal/etc), and leveraging BioPython for format conversion there. Cheers, Eric -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr(a)tamu.edu rasche.eric(a)yandex.ru

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Re: [galaxy-dev] FW: tophat2 failing to execute
by Martin Čech 20 May '15

20 May '15

Hi Eleanora, I am glad the update worked. Please keep the mailing list thread alive by using "reply all". You are missing many smart people thinking about your problem if you don't. :) Let us know how it goes. Martin On Wed, May 20, 2015, 02:52 Eleanor Morgan <E.Morgan(a)curtin.edu.au> wrote: > Hi Martin, > > Apologies. Ignore this message. I needed to update the database, I > expected the script would tell me this up front, but I found the message in > paster.log (which I should have checked first). I’ll get back to you on my > progress with Tophat etc. > > Regards, > Eleanor > > Eleanor Morgan > Senior Scientific Officer | School of Biomedical Sciences | Faculty of > Health Sciences > > > Curtin University > Tel | +61 8 9266 7516 > > Mob | +61 408 004 369 > Fax | +61 8 9266 2342 > Email | e.morgan(a)curtin.edu.au > Web | biomed.curtin.edu.au > > > > Curtin University is a trademark of Curtin University of Technology. > CRICOS Provider Code 00301J (WA), 02637B (NSW) > > > From: Eleanor Morgan <e.morgan(a)curtin.edu.au> > Date: Wednesday, 20 May 2015 1:44 pm > To: Martin Čech <marten(a)bx.psu.edu> > > Subject: Re: [galaxy-dev] tophat2 failing to execute > > Hello Martin, > > Thank you very much for your reply and suggestions. I removed the > /static/scripts/packed folder and reran the update. This time I got > through the process. However, I cannot seem to get galaxy to start up. > As the root user I initiated startup from the init.d/galaxy script > > /etc/init.d/galaxy start > Starting galaxy... > Initializing config/migrated_tools_conf.xml from > migrated_tools_conf.xml.sample > Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample > Initializing config/shed_tool_data_table_conf.xml from > shed_tool_data_table_conf.xml.sample > Initializing config/shed_data_manager_conf.xml from > shed_data_manager_conf.xml.sample > Some eggs are out of date, attempting to fetch... > Fetched http://eggs.galaxyproject.org/repoze.lru/repoze.lru-0.6-py2.6.egg > Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-2.4.1-py2.6.egg > Removed conflicting egg: /galaxy/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg > Fetched http://eggs.galaxyproject.org/sqlparse/sqlparse-0.1.14-py2.6.egg > Fetched http://eggs.galaxyproject.org/amqp/amqp-1.4.6-py2.6.egg > Removed conflicting egg: /galaxy/galaxy-dist/eggs/amqp-1.4.3-py2.6.egg > Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.5.2-py2.6.egg > Removed conflicting egg: /galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.6.egg > Fetched http://eggs.galaxyproject.org/kombu/kombu-3.0.24-py2.6.egg > Removed conflicting egg: /galaxy/galaxy-dist/eggs/kombu-3.0.12-py2.6.egg > Fetched > http://eggs.galaxyproject.org/SQLAlchemy/SQLAlchemy-1.0.1-py2.6-linux-x86_6… > Removed conflicting egg: > /galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg > Fetched http://eggs.galaxyproject.org/Routes/Routes-2.1-py2.6.egg > Removed conflicting egg: /galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg > Fetched http://eggs.galaxyproject.org/six/six-1.9.0-py2.6.egg > Fetched > http://eggs.galaxyproject.org/mercurial/mercurial-3.2.4-py2.6-linux-x86_64-… > Removed conflicting egg: > /galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg > sqlalchemy_migrate 0.9.6 couldn't be downloaded automatically. You can try > building it by hand with: > python scripts/scramble.py -c universe_wsgi.ini -e sqlalchemy_migrate > Fetch failed. > Entering daemon mode > ...done. > > > There appears to be an error since I see Fetch failed. But there is no > message telling me galaxy failed to start. However, there is no evidence > that it is running when I check processes, and the website is not up. > > > I then try stopping and starting > > > [root@binfmt01:/home/175146F]# /etc/init.d/galaxy stop > > Stopping galaxy... No PID file exists in paster.pid > > done. > > [root@binfmt01:/home/175146F]# /etc/init.d/galaxy start > > Starting galaxy... > > Entering daemon mode > > …done. > > > Again, there is no evidence that it is not starting. The web service > does not start up, however and if I check the status I get this: > > /etc/init.d/galaxy status > > galaxy status: stopped > > > Any suggestions on how I can get around this problem will be greatly > appreciated. > > > Regards, > > Eleanor > > > > From: Martin Čech <marten(a)bx.psu.edu> > Date: Wednesday, 20 May 2015 11:52 am > To: Eleanor Morgan <e.morgan(a)curtin.edu.au>, "galaxy-dev(a)lists.bx.psu.edu" > <galaxy-dev(a)lists.bx.psu.edu> > Subject: Re: [galaxy-dev] tophat2 failing to execute > > Hello Eleanor, > > it seems there are multiple issues present. > > First of all in the 15.05 release the static/scripts/packed folder has > been changed to a symlink aiming at static/scripts (this is a part of > internal scriptbuild transition). If it is not a symlink in your filesystem > you can safely remove that folder (static/scripts/packed) with its contents > and update again to receive the correct symlink. That should help you with > the merging of the update. > > Once updated (and please let us know if more trouble arise) we can start > troubleshooting why you canot connect to the Tool Shed (TS). Are you trying > to 'Search and browse tool sheds' in the Admin menu? What is your Galaxy > setup? Are you behind any proxy? What changed since the point at which you > were able to reach TS? > > When it comes to the tophat2 error: the log that can tell you more is > (by default) printed in the console window in which you run Galaxy. If > tophat fails you should see some exceptions or at least a more explicit > error there. > > As a side note it is good to know that the tophat you have locally > installed on your machine is probably not the tophat Galaxy is using while > running the tophat tool. Galaxy will try to use the TS tophat dependency > installed from the package_tophat2_2_0_9. > > Please let us know how it goes. > > Thank you > > Martin, Galaxy Team > > > On Tue, May 19, 2015 at 11:28 PM Eleanor Morgan <E.Morgan(a)curtin.edu.au> > wrote: > >> Hi again, >> >> I didn’t get any response to this so decided to try an upgrade in the >> hope that I could reestablish access to the toolshed. I used bitbucket >> because I was unsure of the implications if I moved to github. Here are >> the commands I issued: >> >> su – galaxy >> >> cd /galaxy/galaxy-dist/ >> >> hg pull >> >> hg update latest_15.05 >> >> >> I was repeatedly asked questions re changing or deleting various >> scripts: >> >> local changed static/scripts/packed/mvc/data.js which remote deleted >> >> use (c)hanged version or (d)elete? C >> >> >> I chose c for all of these >> >> >> Once that finished, the merging process began but eventually ended in >> an error message: >> >> merging static/scripts/nls/zh/locale.js >> >> abort: could not symlink to './': File exists: >> /galaxy/galaxy-dist/static/scripts/packed >> >> >> Any help with this error would be greatly appreciated. Last time I >> updated, I did this from within the galaxy-dist directory >> (/galaxy/galaxy-dist) rather than the root /galaxy directory and it >> worked. Is that correct? >> >> >> Regards, >> >> Eleanor >> >> >> >> Eleanor Morgan >> Senior Scientific Officer | School of Biomedical Sciences | Faculty of >> Health Sciences >> >> >> Curtin University >> Tel | +61 8 9266 7516 >> >> Mob | +61 408 004 369 >> Fax | +61 8 9266 2342 >> Email | e.morgan(a)curtin.edu.au >> Web | biomed.curtin.edu.au >> >> >> >> Curtin University is a trademark of Curtin University of Technology. >> CRICOS Provider Code 00301J (WA), 02637B (NSW) >> >> >> From: Eleanor Morgan <e.morgan(a)curtin.edu.au> >> Date: Tuesday, 19 May 2015 9:50 pm >> To: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> >> Subject: [galaxy-dev] tophat2 failing to execute >> >> Hello, >> >> I am running a local Galaxy install, last update was June, 2014 >> release. I installed Tophat2 from the tool repository some months ago and >> the tool dependency packages for Bowtie2 and Samtools were also installed. >> I have built bowtie2 indices on the human hg19 genome and can select this >> as the reference genome. I am working through a tutorial with paired-end >> sequence reads that works fine on the main galaxy public server. When I >> try to run it on my local instance, however, Tophat2 fails. The error >> reported in the galaxy data window is: >> Fatal error: Tool execution failed >> >> [2015-05-19 21:15:11] Beginning TopHat run (v2.0.9) >> ----------------------------------------------- >> [2015-05-19 21:15:11] Checking for Bowtie >> Bowtie version:2.1.0.0 >> [2015-05-19 21:15:11] Checking for Samtools >> S >> >> >> I checked the tool_dependency.xml file >> >> <tool_dependency> >> >> <package name="bowtie2"version="2.1.0"> >> >> <repository changeset_revision="017a00c265f1"name= >> "package_bowtie2_2_1_0"owner="devteam"prior_installation_required="False" >> toolshed="http://toolshed.g2.bx.psu.edu" /> >> >> </package> >> >> <package name="samtools"version="0.1.18"> >> >> <repository changeset_revision="171cd8bc208d"name= >> "package_samtools_0_1_18"owner="devteam"prior_installation_required= >> "False"toolshed="http://toolshed.g2.bx.psu.edu" /> >> >> </package> >> >> <package name="tophat2"version="2.0.9"> >> >> <repository changeset_revision="8549fd545473"name="package_tophat2 >> _2_0_9"owner="devteam"prior_installation_required="False"toolshed=" >> http://toolshed.g2.bx.psu.edu" /> >> >> </package> >> >> </tool_dependency> >> >> >> All of the listed packages appear to be installed. I am unsure why in >> the run log it is checking for Bowtie instead of Bowtie2, although the >> version is correct for the Bowtie2 package that is installed. >> >> I would like to reinstall everything, but can’t get onto the toolshed >> anymore, I just get a message that I will be redirected, but nothing >> happens. >> >> I am a newbie user of galaxy. Can anyone direct me to a log file that >> might contain more information about why Tophat2 is failing to execute? It >> works fine on the command line. >> >> >> Thanks very much for any advice on what I should check next. >> >> >> Regards, >> >> Eleanor >> >> Eleanor Morgan >> Senior Scientific Officer | School of Biomedical Sciences | Faculty of >> Health Sciences >> >> >> Curtin University >> Tel | +61 8 9266 7516 >> >> Mob | +61 408 004 369 >> Fax | +61 8 9266 2342 >> Email | e.morgan(a)curtin.edu.au >> Web | biomed.curtin.edu.au >> >> >> >> Curtin University is a trademark of Curtin University of Technology. >> CRICOS Provider Code 00301J (WA), 02637B (NSW) >> >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > >

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Re: [galaxy-dev] tophat2 failing to execute
by Eleanor Morgan 19 May '15

19 May '15

Hi again, I didn’t get any response to this so decided to try an upgrade in the hope that I could reestablish access to the toolshed. I used bitbucket because I was unsure of the implications if I moved to github. Here are the commands I issued: su – galaxy cd /galaxy/galaxy-dist/ hg pull hg update latest_15.05 I was repeatedly asked questions re changing or deleting various scripts: local changed static/scripts/packed/mvc/data.js which remote deleted use (c)hanged version or (d)elete? C I chose c for all of these Once that finished, the merging process began but eventually ended in an error message: merging static/scripts/nls/zh/locale.js abort: could not symlink to './': File exists: /galaxy/galaxy-dist/static/scripts/packed Any help with this error would be greatly appreciated. Last time I updated, I did this from within the galaxy-dist directory (/galaxy/galaxy-dist) rather than the root /galaxy directory and it worked. Is that correct? Regards, Eleanor Eleanor Morgan Senior Scientific Officer | School of Biomedical Sciences | Faculty of Health Sciences Curtin University Tel | +61 8 9266 7516 Mob | +61 408 004 369 Fax | +61 8 9266 2342 Email | e.morgan(a)curtin.edu.au<mailto:e.morgan@curtin.edu.au> Web | biomed.curtin.edu.au [cid:8FD8F6A6-991E-469B-899B-F84FF0A57C2A] Curtin University is a trademark of Curtin University of Technology. CRICOS Provider Code 00301J (WA), 02637B (NSW) From: Eleanor Morgan <e.morgan(a)curtin.edu.au<mailto:e.morgan@curtin.edu.au>> Date: Tuesday, 19 May 2015 9:50 pm To: "galaxy-dev(a)lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" <galaxy-dev(a)lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>> Subject: [galaxy-dev] tophat2 failing to execute Hello, I am running a local Galaxy install, last update was June, 2014 release. I installed Tophat2 from the tool repository some months ago and the tool dependency packages for Bowtie2 and Samtools were also installed. I have built bowtie2 indices on the human hg19 genome and can select this as the reference genome. I am working through a tutorial with paired-end sequence reads that works fine on the main galaxy public server. When I try to run it on my local instance, however, Tophat2 fails. The error reported in the galaxy data window is: Fatal error: Tool execution failed [2015-05-19 21:15:11] Beginning TopHat run (v2.0.9) ----------------------------------------------- [2015-05-19 21:15:11] Checking for Bowtie Bowtie version:2.1.0.0 [2015-05-19 21:15:11] Checking for Samtools S I checked the tool_dependency.xml file <tool_dependency> <package name="bowtie2"version="2.1.0"> <repository changeset_revision="017a00c265f1"name="package_bowtie2_2_1_0"owner="devteam"prior_installation_required="False"toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="samtools"version="0.1.18"> <repository changeset_revision="171cd8bc208d"name="package_samtools_0_1_18"owner="devteam"prior_installation_required="False"toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="tophat2"version="2.0.9"> <repository changeset_revision="8549fd545473"name="package_tophat2_2_0_9"owner="devteam"prior_installation_required="False"toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> All of the listed packages appear to be installed. I am unsure why in the run log it is checking for Bowtie instead of Bowtie2, although the version is correct for the Bowtie2 package that is installed. I would like to reinstall everything, but can’t get onto the toolshed anymore, I just get a message that I will be redirected, but nothing happens. I am a newbie user of galaxy. Can anyone direct me to a log file that might contain more information about why Tophat2 is failing to execute? It works fine on the command line. Thanks very much for any advice on what I should check next. Regards, Eleanor Eleanor Morgan Senior Scientific Officer | School of Biomedical Sciences | Faculty of Health Sciences Curtin University Tel | +61 8 9266 7516 Mob | +61 408 004 369 Fax | +61 8 9266 2342 Email | e.morgan(a)curtin.edu.au<mailto:e.morgan@curtin.edu.au> Web | biomed.curtin.edu.au [cid:73AB5085-67E7-491A-AC7A-694821970AA3] Curtin University is a trademark of Curtin University of Technology. CRICOS Provider Code 00301J (WA), 02637B (NSW)

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tophat2 failing to execute
by Eleanor Morgan 19 May '15

19 May '15

Hello, I am running a local Galaxy install, last update was June, 2014 release. I installed Tophat2 from the tool repository some months ago and the tool dependency packages for Bowtie2 and Samtools were also installed. I have built bowtie2 indices on the human hg19 genome and can select this as the reference genome. I am working through a tutorial with paired-end sequence reads that works fine on the main galaxy public server. When I try to run it on my local instance, however, Tophat2 fails. The error reported in the galaxy data window is: Fatal error: Tool execution failed [2015-05-19 21:15:11] Beginning TopHat run (v2.0.9) ----------------------------------------------- [2015-05-19 21:15:11] Checking for Bowtie Bowtie version: 2.1.0.0 [2015-05-19 21:15:11] Checking for Samtools S I checked the tool_dependency.xml file <tool_dependency> <package name="bowtie2" version="2.1.0"> <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.18"> <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="tophat2" version="2.0.9"> <repository changeset_revision="8549fd545473" name="package_tophat2_2_0_9" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> All of the listed packages appear to be installed. I am unsure why in the run log it is checking for Bowtie instead of Bowtie2, although the version is correct for the Bowtie2 package that is installed. I would like to reinstall everything, but can't get onto the toolshed anymore, I just get a message that I will be redirected, but nothing happens. I am a newbie user of galaxy. Can anyone direct me to a log file that might contain more information about why Tophat2 is failing to execute? It works fine on the command line. Thanks very much for any advice on what I should check next. Regards, Eleanor Eleanor Morgan Senior Scientific Officer | School of Biomedical Sciences | Faculty of Health Sciences Curtin University Tel | +61 8 9266 7516 Mob | +61 408 004 369 Fax | +61 8 9266 2342 Email | e.morgan(a)curtin.edu.au<mailto:e.morgan@curtin.edu.au> Web | biomed.curtin.edu.au [cid:73AB5085-67E7-491A-AC7A-694821970AA3] Curtin University is a trademark of Curtin University of Technology. CRICOS Provider Code 00301J (WA), 02637B (NSW)

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simple example of composite data types
by Brian Haas 19 May '15

19 May '15

Greetings. Does anyone per chance have a simple working example of using composite data types? I've gotten as far as I can with the galaxy documentation, and I can't seem to get the additional files bundled into an extra files directory. (note, I have my example submitted w/ files attached, but currently pending moderator approval) much appreciated, ~brian -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

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How to get the dynamically loaded select menus to work in workflows?
by Joanna Parmley 18 May '15

18 May '15

Hi, We have our own local instance of Galaxy from the 15.03.2 release. I have developed a tool that works perfectly well normally but cannot get it integrated into a workflow as we would like. My tool's input form has 3 select menus that use a .loc file (using “from_file” in the options tag) to dynamically load the select options depending on the selected option in the previous field . The problem we see in the workflows happens in the following manner: For the choice of input1 (A or B), there should be a subsequent menu with options for input2 (1,2,3 or 4,5,6 respectively). The select menu input1 is automatically populated with A as this is the first option in the file, and thus the second menu is automatically populated with 1, 2, and 3. However, when you try to select B as input1 the following message is shown: An invalid option was selected for input2, u’1, please verify. The select menu for input1 is then immediately reverted back to A. I can never select B. Is there a way to get the dynamically loaded select menus to work in workflows? Many thanks. Joanna

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