sra-tools in GVL5.0 are not working

[nealfos]

@mvdbeek with the latest galaxy, running on AWS gvl5.0beta5, it seems that fastq_dump is broken.

i have details on what was done below. is this scenario tested and working in the latest release?

I am trying to extract a sample from SRA and getting an error due to certificate signing, the SRR is: SRR1759212

after a while, the tool errors out, the log shows the following error:

mbedtls_ssl_get_verify_result returned 0x8 ( !! The certificate is not correctly signed by the trusted CA )

It seems that there is something wrong with the certificate on the server…

Here is the tool I am using:

I am trying to download the sample:

Job is in queue:

Job is in process:

Here’s the command line that was executed:

Here is the error:

Here are the logs:

[bernt-matthias]

Hi @nealfos .. we also see this error for a while in the weekly tool tests. If I understand the linked issue correctly the suggested solution would be to run the container with docker run -v /etc/pki:/etc/pki:ro -v /etc/ssl:/etc/ssl:ro (btw the tool is not using the ncbi docker container but the one generated by bioconda).

I think this can work on individual Galaxy instance, but it will be difficult to achieve in general, e.g. for the automated tool tests.

Btw. Which Galaxy instance are you using .. we should verify first it the tool is using the container at all or a conda environment.

[nealfos]

I am using the cloudlaunch installer and GVL to run Galaxy on AWS ( https://launch.usegalaxy.org/appliances )

here are the stats:

• Appliance: Genomics Virtual Lab (GVL)
• Version: GVL 5.0 beta5 (Galaxy 20.09)
• Cloud: Amazon Web Services

To be honest, I do not have a development environment to try this out with galaxy sra-tools, but I do know that if i SSH into the AWS machine that is running galaxy, i can run sra-tools using docker run ... so I suspect that it will work.

[bgruening]

ping @afgane could you please have a look? Thanks

[bernt-matthias]

I tested locally wo using containers.

Apparently the same tests are failing. Error messages are Failed to call external services. or for fasterq_dump

...
|  fatal error: An error occurred (404) when calling the HeadObject operation: Key "run/ERR086330/ERR086330" does not exist |  |  Prefetch attempt 1 of 3 exited with code 1
...

[mbargull]

A new Bioconda package and Biocontainer with a fix should be up in an hour or two.