Install via singularity

[oushujun]

Hello,

I don't have sudo privileges on our HPC platform, so I could not use the docker nor the regular installation method. Instead, I am trying to install tephra via singularity.

System confirguations:

Red Hat Enterprise Linux Server 7.6 (Maipo)
Perl version v5.24.1
Singularity version v3.1.1

So I can install tephra using the following command without error:
singularity run docker://sestaton/tephra

Then I type tephra and it shows help info with some warnings for perl:

$tephra
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
Tephra version 0.12.4
Copyright (C) 2015-2019 S. Evan Staton
LICENSE -- MIT
...

I download the tephra_config.yml file and modified the genome name, then run:
tephra all -c tephra_config.yml

I got the following error messages:

perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
Can't load '/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/auto/Bio/DB/HTS/HTS.so' for module Bio::DB::HTS: libhts.so.1: cannot open shared object file: No such file or directory at /usr/lib/x86_64-linux-gnu/perl/5.26/DynaLoader.pm line 187.
at /usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Bio/DB/HTS/Kseq.pm line 71.
Compilation failed in require at /usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Bio/DB/HTS/Kseq.pm line 71.
BEGIN failed--compilation aborted at /usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Bio/DB/HTS/Kseq.pm line 71.
Compilation failed in require at /usr/local/share/perl/5.26.1/Tephra/Stats/Age.pm line 17.
BEGIN failed--compilation aborted at /usr/local/share/perl/5.26.1/Tephra/Stats/Age.pm line 17.
Compilation failed in require at /usr/local/share/perl/5.26.1/Tephra/Command/age.pm line 11.
BEGIN failed--compilation aborted at /usr/local/share/perl/5.26.1/Tephra/Command/age.pm line 11.
Compilation failed in require at /usr/local/share/perl/5.26.1/App/Cmd.pm line 194.
App::Cmd::_command("Tephra", HASH(0x55dfea2ba1e0)) called at /usr/local/share/perl/5.26.1/App/Cmd.pm line 171
App::Cmd::new("Tephra", HASH(0x55dfea2ba1e0)) called at /usr/local/bin/tephra line 25

Is it something wrong with my perl version? Or is it approachable to install it via singularity?

Thanks,
Shujun

[sestaton]

Thanks for the message. I have not tried with singularity yet, but I will take a look this week. From your output it looks to be a locale issue and a problem with loading a shared library.

This is probably something we can fix with a few environment tweaks with singularity, but I'll have to test it out myself and get back to this issue.

[sestaton]

Okay, I can recreate the first issue and resolve it. In singularity, you'll need to run tephra as such:

LANG=C tephra

or

export LANG=C
tephra

I'm not sure if that will resolve the other issue though. Can you try this and test out the full command?
Thanks.

[sestaton]

I can confirm that the above ENV setting alone will not fix the second issue. Will have to explore this further.

[oushujun]

Thank you for working on this. Has this issue being fixed or do you want me to try out the current version?

Shujun

[sestaton]

Thank you for the patience. I could not resolve the issue with trying to load certain compiled C libraries in the Singularity environment that were compiled with the Docker image. But, I have created a new Singularity image and I will try to get that put up ASAP.

[sestaton]

Okay, here are the singularity commands:

singularity pull library://sestaton/default/tephra
LC_ALL=C singularity run tephra_latest.sif 

You will need to bind your data directory with all your files. So, assuming you have a directory in the current directory called data:

LC_ALL=C singularity run --bind $PWD/data:/data tephra_latest.sif

The you can switch to /data and run your analysis. Please let me know this works for you.

[oushujun]

Thank you for making the singularity version available. The installation was smooth:
singularity pull library://sestaton/default/tephra
LC_ALL=C singularity run --bind $PWD/data:/data tephra_latest.sif
cd data
tephra all -c tephra_config.Chr9.yml

Then I encounter these errors:

INFO - ======== Tephra version: 0.12.4 (started at: 25-08-2019 16:48:38) ========
INFO - Configuration - Log file for monitoring progress and errors: tephra_Chr9_full.log
INFO - Configuration - Genome file: Chr9.fasta
INFO - Configuration - Repeat database: dummy071619.fa
INFO - Configuration - Number of threads: 36
INFO - Command - 'tephra findltrs' started at: 25-08-2019 16:48:38.
Copy failed: No such file or directory at /usr/local/share/perl/5.26.1/Tephra/Command/findltrs.pm line 135.
INFO - Command - 'tephra findltrs' completed at: 25-08-2019 16:48:38.
INFO - Command - 'tephra findtrims' started at: 25-08-2019 16:48:38.

[ERROR]: Copy failed: No such file or directory
INFO - Command - 'tephra findtrims' completed at: 25-08-2019 16:48:39.
INFO - Command - 'tephra findhelitrons' started at: 25-08-2019 16:48:39.

[ERROR]: Could not open file: /work/LAS/mhufford-lab/oushujun/TE/TEbenchmark/tephra/data/Chr9_tephra_hscan_helitrons.hel.fa
INFO - Command - 'tephra findhelitrons' completed at: 25-08-2019 16:48:40.
INFO - Command - 'tephra findtirs' started at: 25-08-2019 16:48:40.
Copy failed: No such file or directory at /usr/local/share/perl/5.26.1/Tephra/Command/findtirs.pm line 72.
INFO - Command - 'tephra findtirs' completed at: 25-08-2019 16:48:40.
Use of uninitialized value $tirc_fas in -e at /usr/local/share/perl/5.26.1/Tephra/Command/all.pm line 282.
INFO - Command - 'tephra findnonltrs' started at: 25-08-2019 16:48:40.
No such file or directory /home/oushujun/.tephra/pHMM at /usr/local/share/perl/5.26.1/Tephra/NonLTR/RunHMM.pm line 48.
INFO - Command - 'tephra findnonltrs' completed at: 25-08-2019 16:48:41.
INFO - Command - Generating combined FASTA file of complete elements at: 25-08-2019 16:48:41.
INFO - Results - Finished generating combined FASTA file of complete elements at: 25-08-2019 16:48:41. Final output files:
INFO - Output files - Chr9_tephra_transposons_complete.fasta
INFO - Command - 'tephra maskref' for full-length transposon database started at: 25-08-2019 16:48:41.
sh: 1: /home/oushujun/.tephra/vmatch/mkvtree: not found
sh: 1: /home/oushujun/.tephra/vmatch/mkvtree: not found

Did I forget to configure something?

Thanks!
Shujun