User: harryln

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harryln0
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Posts by harryln

<prev • 10 results • page 1 of 1 • next >
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Comment: C: New data type
... Dear Melanie, I have sorted out this problem by digging into galaxy's tools directory. The uploaded composite file's directory is `input.extra_files_path`. So I can access this directory in my `command` section and change the file names as I need. Many thanks for your help again. You save me a lot t ...
written 12 days ago by harryln0
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Comment: C: New data type
... Dear Melanie, many thanks for your reply. I have upgraded my Galaxy to version of 17.09. So now I can upload imzML (both imzML and ibd) files as a 'composite' file, named as `Uploaded Composite Dataset (imzml)`: imzML Composite Dataset This composite dataset is composed of the following f ...
written 16 days ago by harryln0
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Comment: C: New data type
... Many thanks for your reply. Yes indeed it's a typo. After changing that, I can add the new data type. Unfortunately the uploaded binary data set is *empty* indicated by the History pane. ...
written 16 days ago by harryln0
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NotFound: cannot find 'cluster'
... Hi, I run my tool and get this error massage: Traceback (most recent call last): File "/home/wl/galaxy/lib/galaxy/jobs/runners/__init__.py", line 170, in prepare_job job_wrapper.prepare() File "/home/wl/galaxy/lib/galaxy/jobs/__init__.py", line 864, in prepare self.command_line, self.e ...
datatype galaxy local tool development written 19 days ago by harryln0 • updated 19 days ago by Jennifer Hillman Jackson23k
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Comment: C: New data type
... Dear Hans, yes. I have restarted many times. And I have set the format in my galaxy tool ``` ``` ...
written 19 days ago by harryln0
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New data type
... Hi, I want to upload an imaging binary data file (*.ibd) which contains the mass spectral data (https://ms-imaging.org/wp/imzml/data-structure/) as input. So in my local instance, I need to add a new data type. The followings are my procedures: - In `galaxy/config/datatypes_conf.xml`, I add ` ` ...
dataset datatype config binary admin written 20 days ago by harryln0 • updated 18 days ago by foellmelanie20
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Comment: C: samtools for 32-bit local galaxy
... Dear Jen, I cannot figure out how to sort it out yet. Actually I have nothing to do with `samtools`. I have found galaxy let conda to install `samtools` when uploading CSV data files from local machine. It seems that galaxy try to install `samtools` again and again in a manner of infinite loop, whi ...
written 9 weeks ago by harryln0
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Comment: C: samtools for 32-bit local galaxy
... Hi, Jen, Many thanks for your reply. Use `$ which -a samtools`, the samtools is `/usr/bin/samtools`. The path by `$ echo $PATH` is `/home/wl/bin:/home/wl/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/wl/miniconda3/bin`. But galaxy stil ...
written 10 weeks ago by harryln0
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Comment: A: Mothur not working
... Sorry, mistake. I should reply to Jen for my question. ...
written 10 weeks ago by harryln0
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samtools for 32-bit local galaxy
... My local galaxy instance tries to make conda to install samtools each time when I load data. Unfortunate 32-bit samtools is not available via conda installation. Indeed I have installed samtools by `sudo apt-get install samtools` and it locates in `/usr/bin`. My question is how to let galaxy recogni ...
samtools local path written 10 weeks ago by harryln0 • updated 10 weeks ago by Jennifer Hillman Jackson23k

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