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dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system
https://dib-lab.github.io/elvers/
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Pin version numbers in rule environment.yml files #136

Closed charlesreid1 closed 5 years ago

charlesreid1 commented 5 years ago

This PR pins version numbers in rule environment.yml files, and cleans up some of the syntax in the environment.yml files that already pinned version numbers.

charlesreid1 commented 5 years ago

Hmm, travis is failing with:

UnsatisfiableError: The following specifications were found to be in conflict:
  - bioconductor-deseq2=1.22.1
  - r-gridextra=2.2.1

I think I need to trim some r packages from the environment.yml, as done in #97, rather than just specifying the version of deseq.

charlesreid1 commented 5 years ago

Last error msg from travis build:

CreateCondaEnvironmentException:
Could not create conda environment from /home/travis/miniconda/envs/test-env/lib/python3.6/site-packages/elvers-0.1-py3.6.egg/elvers/rules/deseq2/environment.yml:
Solving environment: ...working... failed
UnsatisfiableError: The following specifications were found to be in conflict:
  - bioconductor-deseq2=1.22.1 -> bioconductor-genomicranges[version='>=1.34.0,<1.35.0'] -> bioconductor-genomeinfodb[version='>=1.18.0,<1.19.0'] -> bioconductor-genomeinfodbdata[version='>=1.2.0,<1.3.0']
  - bioconductor-genomeinfodbdata=1.1.0
Use "conda info <package>" to see the dependencies for each package.
charlesreid1 commented 5 years ago

Now Travis is failing on some deseq2 rules, but no way to access the log file on Travis:

Rscript --vanilla /home/travis/build/dib-lab/elvers/.snakemake/scripts/tmpgw_zjcba.deseq2-init-txOut.R
Activating conda environment: /home/travis/build/dib-lab/elvers/.snakemake/conda/7805c01c
[Tue Apr 16 03:18:39 2019]
Error in rule deseq2_init_txOut:
    jobid: 1
    output: /home/travis/build/dib-lab/elvers/yeast_out/diffexp/yeast_input.deseq2.rds
    log: /home/travis/build/dib-lab/elvers/yeast_out/logs/deseq2/yeast_input.deseq2.init.log (check log file(s) for error message)
    conda-env: /home/travis/build/dib-lab/elvers/.snakemake/conda/7805c01c
Trying to restart job 1.
[Tue Apr 16 03:18:39 2019]
rule deseq2_init_txOut:
    input: /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458502_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458495_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458494_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458500_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458493_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458501_x_yeast_input.salmon/quant.sf
    output: /home/travis/build/dib-lab/elvers/yeast_out/diffexp/yeast_input.deseq2.rds
    log: /home/travis/build/dib-lab/elvers/yeast_out/logs/deseq2/yeast_input.deseq2.init.log
    jobid: 1
    benchmark: /home/travis/build/dib-lab/elvers/yeast_out/logs/deseq2/yeast_input.deseq2.init.benchmark
    wildcards: assembly=yeast_input
Rscript --vanilla /home/travis/build/dib-lab/elvers/.snakemake/scripts/tmp09g8k69v.deseq2-init-txOut.R
Activating conda environment: /home/travis/build/dib-lab/elvers/.snakemake/conda/7805c01c
[Tue Apr 16 03:18:44 2019]
Error in rule deseq2_init_txOut:
    jobid: 1
    output: /home/travis/build/dib-lab/elvers/yeast_out/diffexp/yeast_input.deseq2.rds
    log: /home/travis/build/dib-lab/elvers/yeast_out/logs/deseq2/yeast_input.deseq2.init.log (check log file(s) for error message)
    conda-env: /home/travis/build/dib-lab/elvers/.snakemake/conda/7805c01c
Trying to restart job 1.
[Tue Apr 16 03:18:44 2019]
rule deseq2_init_txOut:
    input: /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458502_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458495_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458494_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458500_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458493_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458501_x_yeast_input.salmon/quant.sf
    output: /home/travis/build/dib-lab/elvers/yeast_out/diffexp/yeast_input.deseq2.rds
    log: /home/travis/build/dib-lab/elvers/yeast_out/logs/deseq2/yeast_input.deseq2.init.log
    jobid: 1
    benchmark: /home/travis/build/dib-lab/elvers/yeast_out/logs/deseq2/yeast_input.deseq2.init.benchmark
    wildcards: assembly=yeast_input
Rscript --vanilla /home/travis/build/dib-lab/elvers/.snakemake/scripts/tmpc2r6ju8d.deseq2-init-txOut.R
Activating conda environment: /home/travis/build/dib-lab/elvers/.snakemake/conda/7805c01c
[Tue Apr 16 03:18:49 2019]
Error in rule deseq2_init_txOut:
    jobid: 1
    output: /home/travis/build/dib-lab/elvers/yeast_out/diffexp/yeast_input.deseq2.rds
    log: /home/travis/build/dib-lab/elvers/yeast_out/logs/deseq2/yeast_input.deseq2.init.log (check log file(s) for error message)
    conda-env: /home/travis/build/dib-lab/elvers/.snakemake/conda/7805c01c
Trying to restart job 1.
[Tue Apr 16 03:18:49 2019]
rule deseq2_init_txOut:
    input: /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458502_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458495_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458494_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458500_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458493_x_yeast_input.salmon/quant.sf, /home/travis/build/dib-lab/elvers/yeast_out/quant/ERR458501_x_yeast_input.salmon/quant.sf
    output: /home/travis/build/dib-lab/elvers/yeast_out/diffexp/yeast_input.deseq2.rds
    log: /home/travis/build/dib-lab/elvers/yeast_out/logs/deseq2/yeast_input.deseq2.init.log
    jobid: 1
    benchmark: /home/travis/build/dib-lab/elvers/yeast_out/logs/deseq2/yeast_input.deseq2.init.benchmark
    wildcards: assembly=yeast_input
Rscript --vanilla /home/travis/build/dib-lab/elvers/.snakemake/scripts/tmps2fbyowp.deseq2-init-txOut.R
Activating conda environment: /home/travis/build/dib-lab/elvers/.snakemake/conda/7805c01c
[Tue Apr 16 03:18:54 2019]
Error in rule deseq2_init_txOut:
    jobid: 1
    output: /home/travis/build/dib-lab/elvers/yeast_out/diffexp/yeast_input.deseq2.rds
    log: /home/travis/build/dib-lab/elvers/yeast_out/logs/deseq2/yeast_input.deseq2.init.log (check log file(s) for error message)
    conda-env: /home/travis/build/dib-lab/elvers/.snakemake/conda/7805c01c
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
  Oh no! Something went wrong here
cat /home/travis/miniconda/envs/test-env/lib/python3.6/site-packages/elvers-0.1-py3.6.egg/elvers/utils/animals/failwhale
     FAIL WHALE!
W     W      W        
W        W  W     W    
              '.  W      
  .-""-._     \ \.--|  
 /       "-..__) .-'   
|     _         /      
\'-.__,   .__.,'       
 `'----'._\--'      
VVVVVVVVVVVVVVVVVVVVV
Complete log: /home/travis/build/dib-lab/elvers/.snakemake/log/2019-04-16T031014.850994.snakemake.log
The command "elvers examples/yeast.yaml quantify diffexp -t 4 --restart_times=3" exited with 1.

Will see if I can get this command working on a vagrant box.