Unable to run HLAthena in the Terra/FireCloud

[Francisco Martinez]

Hi there, 

Congratulations for your work. I'm trying to run HLAthena in a very large dataset of peptides. It seems that the Terra platform does not have loaded the HLAthena workspace... Can you provide a more specific step-by-step tutorial on how to run the software in Terra? Could be possible to download HLAthena software and run it locally (in working in a non-profit research institute)? 

Thanks 

[ang.dion...@gmail.com]

I cannot get Terra to work either. It will be really helpful to provide a downloadable HLAthena.

Thanks

[Sisi Sarkizova]

Hello and thank you for the interest,

I've been looking into this today and created a new demo workspace but as it turned out unfortunately I am not able to share that publicly due to group access restrictions. I will contact and work with the Terra team to resolve this. In the meantime, I will work on providing a pure docker solution that doesn't rely on Terra to execute. I will update you with details in the next few days. This will entail downloading the docker and running a workflow within it. 

Thanks for the patience,

Sisi

[Francisco Martinez]

Hi Sisi, 

Thanks for your reply. I agree that a Terra-independent solution (such as docker container) would be the best possible scenario. Looking forward to it. 

Best, 

[Francisco Martinez]

Hi Sisi, 

Any updates on this? 

Thanks :)

[Sisi Sarkizova]

Apologies for the delay over the holidays. Actively working on a more comprehensive Terra example and will address the stand-alone version next week.

Thanks for the patience!

Sisi

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[Francisco Martinez]

Thanks Sisi for the quick reply. 

Looking forward to the stand-alone version :)

Best

On Thursday, January 2, 2020 at 9:10:35 PM UTC+1, Sisi Sarkizova wrote:

Apologies for the delay over the holidays. Actively working on a more comprehensive Terra example and will address the stand-alone version next week.

Thanks for the patience!

Sisi

On Mon, Dec 30, 2019 at 2:50 PM Francisco Martinez <francisc...@irbbarcelona.org> wrote:

Hi Sisi, 

Any updates on this? 

Thanks :)

On Wednesday, December 18, 2019 at 8:57:23 AM UTC+1, Francisco Martinez wrote:

Hi Sisi, 

Thanks for your reply. I agree that a Terra-independent solution (such as docker container) would be the best possible scenario. Looking forward to it. 

Best, 

On Wednesday, December 18, 2019 at 4:26:20 AM UTC+1, Sisi Sarkizova wrote:

Hello and thank you for the interest,

I've been looking into this today and created a new demo workspace but as it turned out unfortunately I am not able to share that publicly due to group access restrictions. I will contact and work with the Terra team to resolve this. In the meantime, I will work on providing a pure docker solution that doesn't rely on Terra to execute. I will update you with details in the next few days. This will entail downloading the docker and running a workflow within it. 

Thanks for the patience,

Sisi

 

On Tuesday, December 17, 2019 at 4:20:11 PM UTC-5, ang.dio...@gmail.com wrote:

I cannot get Terra to work either. It will be really helpful to provide a downloadable HLAthena.

Thanks

On Tuesday, December 17, 2019 at 4:11:50 AM UTC-5, Francisco Martinez wrote:

Hi there, 

Congratulations for your work. I'm trying to run HLAthena in a very large dataset of peptides. It seems that the Terra platform does not have loaded the HLAthena workspace... Can you provide a more specific step-by-step tutorial on how to run the software in Terra? Could be possible to download HLAthena software and run it locally (in working in a non-profit research institute)? 

Thanks 

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[Laurenz...@ugent.be]

Dear S. Sarkizova,

My apologies for disturbing you. I was, however, wondering whether there were any updates regarding the stand-alone version?

Kind regards,

Laurenz De Cock

On Thursday, January 2, 2020 at 9:10:35 PM UTC+1, Sisi Sarkizova wrote:

Apologies for the delay over the holidays. Actively working on a more comprehensive Terra example and will address the stand-alone version next week.

Thanks for the patience!

Sisi

On Mon, Dec 30, 2019 at 2:50 PM Francisco Martinez <francisc...@irbbarcelona.org> wrote:

Hi Sisi, 

Any updates on this? 

Thanks :)

On Wednesday, December 18, 2019 at 8:57:23 AM UTC+1, Francisco Martinez wrote:

Hi Sisi, 

Thanks for your reply. I agree that a Terra-independent solution (such as docker container) would be the best possible scenario. Looking forward to it. 

Best, 

On Wednesday, December 18, 2019 at 4:26:20 AM UTC+1, Sisi Sarkizova wrote:

Hello and thank you for the interest,

I've been looking into this today and created a new demo workspace but as it turned out unfortunately I am not able to share that publicly due to group access restrictions. I will contact and work with the Terra team to resolve this. In the meantime, I will work on providing a pure docker solution that doesn't rely on Terra to execute. I will update you with details in the next few days. This will entail downloading the docker and running a workflow within it. 

Thanks for the patience,

Sisi

 

On Tuesday, December 17, 2019 at 4:20:11 PM UTC-5, ang.dio...@gmail.com wrote:

I cannot get Terra to work either. It will be really helpful to provide a downloadable HLAthena.

Thanks

On Tuesday, December 17, 2019 at 4:11:50 AM UTC-5, Francisco Martinez wrote:

Hi there, 

Congratulations for your work. I'm trying to run HLAthena in a very large dataset of peptides. It seems that the Terra platform does not have loaded the HLAthena workspace... Can you provide a more specific step-by-step tutorial on how to run the software in Terra? Could be possible to download HLAthena software and run it locally (in working in a non-profit research institute)? 

Thanks 

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[Sisi Sarkizova]

Dear Laurenz, 

Thank you for reaching out, updates to the thread have gotten lost as the group was dropped. Please try the following:

We have developed a stand-alone docker-based solution which is still undergoing minor tweaks but a version is already available to try. Please follow the following instruction:

Please pull the following docker image (assuming you already have docker installed):
      docker pull ssarkizova/hlathena-external

Then run:
    docker run -v `pwd`:`pwd` -w `pwd` ssarkizova/hlathena-external predict --help

You should see help output with run examples and descriptions of the available options. The parameters are very similar to those on the website and the examples should hopefully explain how to build up the command for your use case. More details on the input and output formats are available on the website: Predict -> How to.

Hope this helps, let me know if you have any questions.

Sisi

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[zhewe...@gmail.com]

Hi Sisi:

Thank you for providing docker version of Hlathena tools. I have pulled that image and run command as you recommend in examples, such like

' docker run -v `pwd`:`pwd` -w `pwd` ssarkizova/hlathena-external predict --runID test --rundir ./test/ --peptides ./test/sample_input_peptides.txt --alleles A1101'

here, the 'sample_input_peptides.txt'  is sample input provided on hlathena website version. However, the runinning time is long for this command and it generated a tmp dir with 'peps.8.txt'、 ‘peps.8.txt`、  `test-out.log`. And I didn't get 'test.txt' as expecting  output file. In the 'test-out.log', I got error like this:

Could you please help me to figure out solution for this problem? I would appreciate for that.

best, 

Shawn.Song

在 2020年3月26日星期四 UTC+8上午8:36:20，Sisi Sarkizova写道：

Dear Laurenz, 

Thank you for reaching out, updates to the thread have gotten lost as the group was dropped. Please try the following:

We have developed a stand-alone docker-based solution which is still undergoing minor tweaks but a version is already available to try. Please follow the following instruction:

Please pull the following docker image (assuming you already have docker installed):
      docker pull ssarkizova/hlathena-external

Then run:
    docker run -v `pwd`:`pwd` -w `pwd` ssarkizova/hlathena-external predict --help

You should see help output with run examples and descriptions of the available options. The parameters are very similar to those on the website and the examples should hopefully explain how to build up the command for your use case. More details on the input and output formats are available on the website: Predict -> How to.

Hope this helps, let me know if you have any questions.

Sisi

To view this discussion on the web visit https://groups.google.com/d/msgid/hlathena/fbf83fe1-349e-444c-89e7-5f3b647d784f%40googlegroups.com.

[HLAthena Team]

Hi Shawn.Song,

It seems like the docker is not able to pull the models from the google bucket to the local system. Does the machine have external web access?

Best,

Sisi

[zhewe...@gmail.com]

Hi Sisi:

I accessed my network to external web. Your tools worked for me!! Thanks for your help!!

best,

Shawn.Song

在 2020年5月7日星期四 UTC+8上午12:41:06，HLAthena Team写道：

[Sisi Sarkizova]

Great, thanks for letting me know!

Sisi

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[zhewe...@gmail.com]

Hi Sisi:

  

       I met some error in test-out.log " rm: cannot remove 'clevnnfeats.tmp': No such file or directory" , when I use optional term '--run_ctex true' .  Could you please check whether this is a common error ? Since I tried several dataset which all raise this error. Thanks

best, 

Shawn.Song

在 2020年5月8日星期五 UTC+8上午6:43:09，Sisi Sarkizova写道：

To view this discussion on the web visit https://groups.google.com/d/msgid/hlathena/c49b53b0-9d2c-40b7-b274-b9a8b2f8972c%40googlegroups.com.