gatk install difficulty

[jb013b]

I am having a problem installing gatk

As you can tell I am new to linux Ubuntu 14lts I installed the viral-ngs pipeline using the easy deploy shell script. I can activate the viral-ngs environment and I made the mkdir -p /path/to/gatk_dir the wget line fails. I recorded the terminal during the install and pasted that below. I can see the gatk_dir so that worked I also have several copies of the gatk.tar after a few different attempts but keep running into problems

Any help appreciated.

Best, James

Script started on Fri 08 Dec 2017 01:24:51 PM CST ]0;jb013b@jb013b-OptiPlex-9020: ~/Documentsjb013b@jb013b-OptiPlex-9020:~/Documents$ cd ~ ]0;jb013b@jb013b-OptiPlex-9020: ~jb013b@jb013b-OptiPlex-9020:~$ source activate viral-ngs-env (viral-ngs-env) ]0;jb013b@jb013b-OptiPlex-9020: ~jb013b@jb013b-OptiPlex-9020:~$ wget -O - 'https://software.broadinstitute.org/gatk/down load/auth?package=GATK-archive&version=3.6-0-g89b7209' | tar -xjvC /path/to/gatk_dir --2017-12-08 13:25:32-- https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.6-0-g89b7209 Resolving software.broadinstitute.org (software.broadinstitute.org)... 69.173.92.37 Connecting to software.broadinstitute.org (software.broadinstitute.org)|69.173.92.37|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 12610798 (12M) [application/octet-stream] Saving to: ‘STDOUT’

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2017-12-08 13:25:47 (842 KB/s) - written to stdout [12610798/12610798]

tar: GenomeAnalysisTK.jar: Cannot open: Permission denied resources/exampleFASTA.dict tar: resources: Cannot mkdir: Permission denied tar: resources/exampleFASTA.dict: Cannot open: No such file or directory resources/exampleFASTA.fasta tar: resources: Cannot mkdir: Permission denied tar: resources/exampleFASTA.fasta: Cannot open: No such file or directory resources/exampleBAM.bam tar: resources: Cannot mkdir: Permission denied tar: resources/exampleBAM.bam: Cannot open: No such file or directory resources/exampleBAM.bam.bai tar: resources: Cannot mkdir: Permission denied tar: resources/exampleBAM.bam.bai: Cannot open: No such file or directory resources/exampleFASTA.fasta.fai tar: resources: Cannot mkdir: Permission denied tar: resources/exampleFASTA.fasta.fai: Cannot open: No such file or directory tar: Exiting with failure status due to previous errors (viral-ngs-env) ]0;jb013b@jb013b-OptiPlex-9020: ~jb013b@jb013b-OptiPlex-9020:~$ gatk-register /path/to/gatk_dir/GenomeAnalysisTK.jar ENV_PREFIX /home/jb013b/miniconda3/envs/viral-ngs-env Processing GenomeAnalysisTK.jar as *.jar Error: Unable to access jarfile /path/to/gatk_dir/GenomeAnalysisTK.jar The version of the jar specified, , does not match the version expected by conda: 3.6 (viral-ngs-env) ]0;jb013b@jb013b-OptiPlex-9020: ~jb013b@jb013b-OptiPlex-9020:~$ exit exit

Script done on Fri 08 Dec 2017 01:26:26 PM CST

[tomkinsc]

When you call gatk-register, you need to replace the placeholder path used in the help text, /path/to/gatk_dir/GenomeAnalysisTK.jar, with the actual location of GenomeAnalysisTK.jar on your machine.

[jb013b]

Chris,

Thank you. I got it.

Another question. I am working through the readthedocs files.

Is there a set of test data (sequences) to work through the Snakemake pipeline, and compare my results to what has been run in the past.

I hope you have a great weekend.

Once again. Thank you

James

From: Chris Tomkins-Tinch notifications@github.com Reply-To: broadinstitute/viral-ngs-deploy reply@reply.github.com Date: Friday, December 8, 2017 at 1:50 PM To: broadinstitute/viral-ngs-deploy viral-ngs-deploy@noreply.github.com Cc: James Brien jb013b@gmail.com, Author author@noreply.github.com Subject: Re: [broadinstitute/viral-ngs-deploy] gatk install difficulty (#56)

When you call gatk-register, you need to replace the placeholder path used in the help text, /path/to/gatk_dir/GenomeAnalysisTK.jar, with the actual location of GenomeAnalysisTK.jar on your machine.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[tomkinsc]

You can run some of the integration tests to check that the output should be what is expected for your installation. A command to run would be:

pytest test/integration/test_assembly.py

This makes use of the .bam and .fasta files found within test/input/

[jb013b]

Hi Chris, Thank you for your help. I have run into a few other problems/questions. Please let me know if it is best to post this on github.

I tried the pytest above and it did not work.

I have used the easy deploy script which ran without any problems.

./easy-deploy-viral-ngs.sh setup

I activated the viral-ngs environment source ./easy-deploy-viral-ngs.sh load

I have installed and tested GATK and registered it within the conda viral-ngs env. I installed pytest while in my home directory (not in conda viral-ngs env)

I have attached a document that has me activate the conda env and trying to run the pytest attached.

One other thing that maybe related. I did a clean install of the ubuntu system and started from scratch with the conda install with the easy deploy script, rather than a manual install. Since the clean install I have to use source ./easy-deploy-viral-ngs.sh load to activate the conda env.

I am trying to work towards using the snakemake pipeline.

I greatly appreciate your help.

Best James Saint Louis University

On Fri, Dec 8, 2017 at 3:07 PM, Chris Tomkins-Tinch < notifications@github.com> wrote:

You can run some of the integration tests to check that the output should be what is expected for your installation. A command to run would be:

pytest test/integration/test_assembly.py

This makes use of the .bam and .fasta files found within test/input/ https://github.com/broadinstitute/viral-ngs/tree/master/test/input

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/viral-ngs-deploy/issues/56#issuecomment-350371944, or mute the thread https://github.com/notifications/unsubscribe-auth/Af-JUqq8unKkE2uT_FOqElB4o3EnU0t4ks5s-aUOgaJpZM4Q7jsz .

[tomkinsc]

Hi James, It looks like your attachment didn't make it through to GitHub from your email. If you upload it on the website I can take a look. The easy deploy script does a few different things. First it installs an isolated copy of miniconda in a subdirectory, then creates the viral-ngs conda environment. Viral-ngs and all of its dependencies are installed to the latter environment. To run pytest on viral-ngs, you can install the pytest and the other test dependencies via conda install --file requirements-conda-tests.txt with the viral-ngs conda environment active. That should install pytest and the related dependencies in a way that viral-ngs can be tested.

[jb013b]

Hi Chris, Thank you for the help. I got it to work today. I wound up using conda install pytest, the line above did not wind up working. I ran the pytest and it says 5 passed and 1 skipped.

A few more questions.

Should I always initiate the source with: source ./easy-deploy-viral-ngs.sh load

What reading you recommend to get the snakemake up and running?

I have the readthedocs material. I also have read the older vphaser/2 and vicuna manuscripts. Any other suggestions or places to look.

Once again I greatly appreciate the help and hope you have a happy holidays.

Best, James

On Thu, Dec 14, 2017 at 10:45 AM, Chris Tomkins-Tinch < notifications@github.com> wrote:

Hi James, It looks like your attachment didn't make it through to GitHub from your email. If you upload it on the website I can take a look. The easy deploy script does a few different things. First it installs an isolated copy of miniconda in a subdirectory, then creates the viral-ngs conda environment. Viral-ngs and all of its dependencies are installed to the latter environment. To run pytest on viral-ngs, you can install the pytest and the other test dependencies via conda install --file requirements-conda-tests.txt with the viral-ngs conda environment active. That should install pytest and the related dependencies in a way that viral-ngs can be tested.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/viral-ngs-deploy/issues/56#issuecomment-351767251, or mute the thread https://github.com/notifications/unsubscribe-auth/Af-JUr081C7LQcmAjLQIuE2HFyRZE70Jks5tAVCsgaJpZM4Q7jsz .