User: Inquirer

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Inquirer80
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Posts by Inquirer

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Error uploading Galaxy file via HTTP
... Hi, thanks for the reply. I am using the following in bioblend: ``` gi = GalaxyInstance(url = GALAXY_URL, key=key_admin) gi.libraries.upload_from_galaxy_filesystem(library_id=library_id,filesystem_paths=filepath,link_data_only='link_to_files') ``` As I said, this works fine. In PHP, the file is se ...
written 5 months ago by Inquirer80
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Error uploading Galaxy file via HTTP
... Hi, In our facility we have a web server that uploads files to Galaxy libraries via HTTP requests in PHP. It has been working for a while, but following an update to the latest version of Galaxy it started returning this error: ``` Fatal error: Exit code 1 () Traceback (most recent call last): F ...
http galaxy upload api written 5 months ago by Inquirer80
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(Closed) DAVID missing from the Galaxy toolshed?
... Hi everyone, I have noticed that the DAVID wrapper is not available on the Tool Shed, despite the fact that the tool can be used in the Galaxy Main instance. I have only been able to find some other instances that use it, as well as a [post on the Galaxy Dev List][1] of a user who was also looking ...
galaxy functional annotation written 20 months ago by Inquirer80
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Comment: C: Error installing 'perl' dependency
... Thanks for the suggestion, but it does not seem to work. The Ubuntu package `libexpat-dev` was already installed on my machine and adding `expat` did not help either. Also, the error seems to affect other packages besides `package_perl_xml_parser_expat_2_41`, so I am not sure this is exactly the pro ...
written 23 months ago by Inquirer80
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Error installing 'perl' dependency
... Hello everyone. I encounter an error whenever I try to install any repositories that have the 'perl' dependency, such as 'package_bioperl_1_6' or 'package_perl_xml_parser_expat_2_41'. In all cases I get an error similar to this one: > **Tool shed repository:** package_perl_xml_parser_expat_2_41 ...
error dependencies toolshed perl written 23 months ago by Inquirer80 • updated 16 months ago by jakeflood0
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Comment: C: Newest FASTQC repository not containing any dependencies
... Indeed, I changed it manually at some point. I first installed conda in `database/dependencies/_conda` because I had issues with the automatic installation, as reported above. After I fixed some apparently malformed lines in my Galaxy.ini file, I changed the `conda_prefix` to `database/dependencies/ ...
written 23 months ago by Inquirer80
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Comment: C: Newest FASTQC repository not containing any dependencies
... Hi again. Sorry for coming back with the same, but now I am having trouble running the FASTQC version with Conda dependencies. To be honest I don't remember if I ever managed to do so, or I just assumed everything was fine when I saw that dependencies had been installed by Conda in the `Dependency R ...
written 23 months ago by Inquirer80
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Comment: C: Newest FASTQC repository not containing any dependencies
... I have tried once more and this time Galaxy was capable of installing Conda by itself. I am not sure what I did wrong the last time, but it works. Sorry for the unjustified alarm. ...
written 23 months ago by Inquirer80
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Comment: C: Data Managers not containing uploaded data? (hg38 missing)
... Now I get it! Thanks a lot! ...
written 23 months ago by Inquirer80
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Data Managers not containing uploaded data? (hg38 missing)
... Hi everyone, I am trying to load some reference genomes onto our Galaxy production server. Following the advice provided on this forum (for instance, https://biostar.usegalaxy.org/p/19371/), I tried to use data managers to that purpose, but they only display reference genomes release until 2010. I ...
data manager alignment tool reference genome written 23 months ago by Inquirer80 • updated 23 months ago by Jennifer Hillman Jackson25k

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Student 20 months ago, asked a question with at least 3 up-votes. For Error installing 'perl' dependency

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