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Building from source issues - Is TypeTE Docker container ready? #2
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Dear Matthiew, Thank you for your interest! I'm so sorry, indeed this repos is a dev version that is not functional. It's not on your end! For the use of TypeTE as in the paper, I recommend to use the github. Be sure that you have bioperl properly installed because it is a source of problems. We are currently working to improve the deletion pipeline (reference insertions) and this will be integrated with nextflow/docker. However we need a few more months on the dev! Best, Clément |
By the way, I just found you v a p o R w a v e package and I love it! I'm gonna try it out for my next presentation! =) |
Reading your issue again, I wonder if this is not related to the PERL5LIB variable which doesn't points toward local libraries. I am not a perl expert, but maybe @jainy who coded the perl scripts can help you! Best, Clément |
Hi Matthiew, Can you try to install String::Approx using an alternative method and check if that works. perl -MCPAN -e shell Thanks |
Hi @jainy Where does Here is what I see inside the
These don't look like
As I mentioned, there is no outgoing internet connection on this server so I can install
Where each module folder looks like:
Now, when I look on the laptop where I installed with your method I can find
Okay let's take a look back on the secure linux in the
Above, I've cut-off most of the output, however, two things are apparent/confusing:
Therefore, I tried to copy over this And @clemgoub, on your point about the possibility of it being related to
In the error log, we see that no error is raised for
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Hi Matthiew, I am not sure. I found a webpage that describes the installation of perl modules locally. Can you try that. https://blogs.iu.edu/ncgas/2019/05/30/installing-perl-modules-locally/ This describes how to get the String::Approx and install locally and add that path to the bashrc file as needed. Hope it helps! Best, |
That is exactly the process I described above... |
Hi Matthiew, I am sorry if I am repeating myself. wget https://cpan.metacpan.org/authors/id/J/JH/JHI/String-Approx-3.28.tar.gz Best, |
@jainy yes, here were the commands I used:
Here is a bit different than the instructions because it's failing with the
Let's confirm it work from the LOGIN node:
Looks like it works there. Now try submitting a script and make sure to include the environmental variables that affect
And I get the following error:
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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
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 downloadPerl
modules. After downloading/installing all the dependencies listed I rantypeTE
and recieved errors about missing Perl moduleBio::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.Then I transfer this to the secure computing environment into my
perl5
directory andtar zxvf BioPerl-1.7.8.tar.gz && cd BioPerl
, followed by buildingperl Makefile.PL
. I will then verify the installation withperl -e "use Bio::SeqIO
(if I don't see errors that means it's installed).Next try to run
typeTE
again but I get an error aboutString::Approx
so I follow the same method described, followed byperl -e "use String::Approx qw(amatch);"
- things appear to be installed:I add both the
perl -e
statements now to the top of my batch script and try to runtypeTE
and here is where the odd behavior is happening:Script
As you can see I've commented out the
run_TypeTE_Ref.sh
script and the first call toBio::Seq
runs successfully without error; however, the call toString::Approx
throws an error.Error
Albeit, not directly a
typeTE
issue, this issue with theString::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
)The text was updated successfully, but these errors were encountered: