Building from source issues - Is TypeTE Docker container ready?

[moldach]

As I'm working with patient data (level 4 data) we're on a secure Linux compute cluster where, for security reasons, it is not possible to make outbound connections to the internet.

Originally I had tried building from source, however, I ran into major issues with the installation of a particular Perl dependency (see notes at bottom) therefore I would like to run the Docker container for TypeTE but not sure if it's ready or not?

me not knowing how to use the container

sudo docker pull cgoubert/typete
sudo docker run -it --entrypoint /home/TypeTE/softwares/TypeTE/ cgoubert/typete run_TypeTE_NRef.sh &> TypeTE.log &

Doesn't look running this container would be straight-forward, so if it's functional some documentation would be greatly helpful.

Issues with building from source

As I have no outbound connection to the internet I cannot use pip to download Perl modules. After downloading/installing all the dependencies listed I ran typeTE and recieved errors about missing Perl module Bio::SeqIO so I have to do the following.

First, I grab the link for the module from meta::cpan website on a laptop with internet connection.

wget https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.7.8.tar.gz

Then I transfer this to the secure computing environment into my perl5 directory and tar zxvf BioPerl-1.7.8.tar.gz && cd BioPerl, followed by building perl Makefile.PL. I will then verify the installation with perl -e "use Bio::SeqIO (if I don't see errors that means it's installed).

[moldach@marc TypeTE-Test]$ perl -e "use Bio::SeqIO;"
[moldach@marc TypeTE-Test]$

Next try to run typeTE again but I get an error about String::Approx so I follow the same method described, followed by perl -e "use String::Approx qw(amatch);" - things appear to be installed:

 [moldach@marc TypeTE-Test]$ perl -e "use String::Approx qw(amatch);"
[moldach@marc TypeTE-Test]$

I add both the perl -e statements now to the top of my batch script and try to run typeTE and here is where the odd behavior is happening:

Script

#!/bin/bash
#SBATCH --job-name=typeTE_test # Job name
#SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH [email protected] # Where to send mail
#SBATCH --ntasks=1 #Run on a single CPU
#SBATCH --cpus-per-task=1 # How many cores?
#SBATCH --mem-per-cpu=1G
#SBATCH --output=typeTE_test_%j.log # Standard output and error log
#SBATCH --error=typeTE_test_%j.err # Error log
#SBATCH --time=01:00:00
pwd; hostname; date

perl -e "use Bio::Seq"
perl -e "use String::Approx"

#bash run_TypeTE_Ref.sh

date

As you can see I've commented out the run_TypeTE_Ref.sh script and the first call to Bio::Seq runs successfully without error; however, the call to String::Approx throws an error.

Error

Can't locate String/Approx.pm in @INC (you may need to install the String::Approx module) (@INC contains: /project/M-mtgraovac182840/perl5-matt/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5) at -e line 1.
BEGIN failed--compilation aborted at -e line 1.

Albeit, not directly a typeTE issue, this issue with the String::Approx Perl module dependency in the linchpin preventing me from using this tool.

While we are fairly new to working in this restrictive environment I have successfully installed 15 other Perl modules into /project/M-mtgraovac182840/perl5-matt/, by running the install process described above (e.g. tar ... && cd ... && perl Makefile.pl)