User: harryln

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harryln10
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Posts by harryln

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An error occurred with this dataset
... Dear all, I have this message: *An error occurred with this dataset* after running Galaxy. The results in my local `~/galaxy/database/files/000` are fine. Even I can `View` and `Download` these results from Galaxy GUI's `History` panel. There are no any error messages indicating my R scripts are wr ...
galaxy software error written 10 weeks ago by harryln10 • updated 8 weeks ago by Jennifer Hillman Jackson25k
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Answer: A: Uploaded filename extension
... Dear Jennifer, Many thanks for your reply. Actually my input is mzML, not Excel data. Instead of renaming file extension, I link these files to mzML after searching other people's galaxy codes by: ``` #for $file in $mzxml_file: ln -s ${file} ${file}.mzXML && #end for ``` Many thank ...
written 10 weeks ago by harryln10
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Uploaded filename extension
... Dear Sir/Madam, I use 'Get Data' to upload a bunch of mzXML files. The uploaded file extension is changed as '.dat'. Unfortunately my software cannot accept this extension. Would someone kindly tell me how to rename back these multiples' extension in `...` section or just upload files while keeping ...
datatype galaxy upload written 10 weeks ago by harryln10
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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 10 months ago by harryln10
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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 11 months ago by harryln10
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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 11 months ago by harryln10
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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 11 months ago by harryln10 • updated 11 months ago by Jennifer Hillman Jackson25k
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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 11 months ago by harryln10
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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 11 months ago by harryln10 • updated 10 months 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 12 months ago by harryln10

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