[JOSS REVIEW] Installation fails

[tkchafin]

This is a part of the JOSS review (https://github.com/openjournals/joss-reviews/issues/6272)

---

On first attempt I get an issue with missing anaconda-client

(base) tyler@Tylers-MacBook-Pro-2 intronSeeker % CONDA_SOLVER="libmamba" /bin/bash ./setup.sh

### Begin installing intronSeeker...

### Conda environment installing... 

SpecNotFound: Anaconda Client is required to interact with anaconda.org or an Anaconda API. Please run `conda install anaconda-client -n base`.

FAIL : Conda environment installation FAILED.

If I manually install anaconda-client I get an issue about needing to log in, but I think this is because setup.sh is not correctly resolving the path to the environment.yml file:

### Begin installing intronSeeker...

### Conda environment installing... 

SpecNotFound: (3)/Downloads/intronSeeker/config/environment.yml was not found on anaconda.org.
You may need to be logged in. Try running:
    anaconda login

FAIL : Conda environment installation FAILED.

Output of pwd:

(base) tyler@Tylers-MacBook-Pro-2 intronSeeker % pwd
/Users/tyler/Downloads/intronSeeker

So I'm not sure where the "(3)/" is coming from. Is it not possible to make this installable directly via conda? Like: conda -c YOUR_CHANNEL intronSeeker

[CFGrote]

Installation fails here, too.

Running setup.sh aborted. I then ran the various perl install steps in the script manually. Here's where it failed;

▶ ls
Getopt-Euclid-0.4.5  Getopt-Euclid-0.4.5.tar.gz  Math-Random-MT-1.17  Math-Random-MT-1.17.tar.gz  Test-Number-Delta-1.06  Test-Number-Delta-1.06.tar.gz
(ISeeker_environment) 
envs/ISeeker_environment/tmp                                                                                                                                                                                                                                                                                      
▶ cd Math-Random-MT-1.17 
(ISeeker_environment) 
ISeeker_environment/tmp/Math-Random-MT-1.17                                                                                                                                                                                                                                                                       
▶ perl Makefile.PL 
Generating a Unix-style Makefile
Writing Makefile for Math::Random::MT
Writing MYMETA.yml and MYMETA.json
(ISeeker_environment) 
ISeeker_environment/tmp/Math-Random-MT-1.17                                                                                                                                                                                                                                                                       
▶ make
Skip blib/lib/Math/Random/MT.pm (unchanged)
Running Mkbootstrap for MT ()
chmod 644 "MT.bs"
"/scratch/grotec/mambaforge/envs/ISeeker_environment/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- MT.bs blib/arch/auto/Math/Random/MT/MT.bs 644
/scratch/grotec/mambaforge/envs/ISeeker_environment/bin/..//bin/x86_64-conda-linux-gnu-gcc -c   -D_REENTRANT -D_GNU_SOURCE --sysroot=/scratch/grotec/mambaforge/envs/ISeeker_environment/bin/..//x86_64-conda-linux-gnu/sysroot -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2   -DVERSION=\"1.17\" -DXS_VERSION=\"1.17\" -fPIC --sysroot=/scratch/grotec/mambaforge/envs/ISeeker_environment/bin/..//x86_64-conda-linux-gnu/sysroot "-I/scratch/grotec/mambaforge/envs/ISeeker_environment/lib/5.26.2/x86_64-linux-thread-multi/CORE"   MT.c
In file included from /scratch/grotec/mambaforge/envs/ISeeker_environment/lib/5.26.2/x86_64-linux-thread-multi/CORE/op.h:654,
                 from /scratch/grotec/mambaforge/envs/ISeeker_environment/lib/5.26.2/x86_64-linux-thread-multi/CORE/perl.h:3921,
                 from MT.xs:2:
/scratch/grotec/mambaforge/envs/ISeeker_environment/lib/5.26.2/x86_64-linux-thread-multi/CORE/reentr.h:104:17: fatal error: crypt.h: No such file or directory
  104 | #       include <crypt.h>
      |                 ^~~~~~~~~
compilation terminated.
make: *** [Makefile:336: MT.o] Error 1
(ISeeker_environment) 
ISeeker_environment/tmp/Math-Random-MT-1.17                                                                                                                                                                                                                                                                      ⍉
▶ 

[pbordron]

We thank you for the comments about creating a conda channel.

Conda Channel

We will create a conda channel providing dependencies missing from conda-forge and bioconda channels. This will allow an easier installation of intronSeeker dependencies for the review, waiting that those packages are accepted into conda-forge and bioconda channels.

We already have the build recipes available

We will naturally update the installation instructions to reflect those updates.

crypt.h issue

This issue is related to some conda-forge sysroot package modification. Our conda packages manage this build issue.

---

@CFGrote @tkchafin We'll notify you as soon as it's available.

[Bios4Biol]

@CFGrote @tkchafin , the installation procedure has been modified with the use of an intronSeeker conda channel. The INSTALL.md file has been updated and it is now possible to test the intronSeeker installation as well as intronSeeker. Only the last “FindEvidence” step is still being tested on our side. Thank you again.