Galaxy - How to access the command line used to execute a tool

Hey, is there any way I can visualize the command line that Galaxy is using to run the tool? I am interested in the command line for Filter BAM/SAM - by region. I managed to do it with the command samtools view, however I can’t make another BAM file.

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If you click the ‘I’ icon on a datasets detailed information section it will give you the command line used to create that dataset.

You may not have permission to view the command line on all Galaxy instances.


Is there any way I can get the permission?

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Not on any public instance, it might reveal sensitive information about the server.

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Alright. Thanks.

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@innovate-invent Great advice! :slight_smile:

@Sammy Few other options …

Many tools will include the command-line in a bug report. If the public Galaxy server allows you to send one in, you’ll get a copy cc’d. The idea is to 1) Make the tool error on purpose 2) Send in the bug report and state in the comments that the error was done on purpose to inspect the job command line (lets the server admins know that you do not need help solving some true job error).

The above will not work at all Public Galaxy servers or tools. Either because of the way permissions are set or because the tool itself does not report the command-line in bug reports (generally older tools).

And… you could always set up a simple local Galaxy, become admin, install the tool, run it with small data (the test data for the tool is usually a good choice), and gain full access to the “Job Details” report (i icon) after the job completes.

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Thanks for the answer. Right, so now I have a local instance of Galaxy. I installed some tools that I am interested in. I want to run some aligners. Are there any indexed human reference genomes that won’t take that much space to upload them? I want to run some tests.

I searched but I don’t think they exist:(. I barely have any memory for this kind of jobs.

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@Sammy Human fasta + indexes will be very large and take up space on disk, whether you create these indexes yourself (Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting) or import pre-compiled indexes (

If you do have space for the indexes, there may be downstream problems if there is limited RAM. Meaning, tools can fail later for memory resources. Tools use the same amount of RAM whether run in Galaxy or line-command. How much RAM a tool uses depends on a few factors: how the tool itself handles data, tool parameters, input sizes, input content…

See the underlying tool’s manual for how much RAM is recommended – most will have a link to the source tool’s home page or try a google search.

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I am gonna have access to a server soon where, probably I am going to use HISAT2 tool so I am trying to understand how it works.

I took a look at HISAT2 command line and I have a really important question:

  • in Galaxy, I am using a build in reference genome (Human Genome 38). Does HISAT2 align the reads against the entire human genome? How can I make sure that I am doing the same in the HISAT2 command line? I could not find the human fasta in one file.

The command line would be:
hisat2-buld [options] <reference_in> <ht2_base>

where <reference_in> is a comma-separated list of FASTA files containing the reference genome sequences to be aligned to.

Where can I download the <reference_in> from? I found only separate files for each chromosome. For the purpose of my study, I need to use the entire genome.

Nevermind, stupid question. I just read the hisat2-build documentation. I just use as an input different fasta files, comma separated. :slight_smile:

Like I said here actually:))) That was a wild ride:))

@Sammy I believe on you can see the command line.

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