AGAT cannot access features_level1.json file (wrong shared folder location detected by File::Share)

wuxiaopei0509 commented 4 years ago

Hi,Juke I use agat_sp_gxf_to_gff3.pl to convert the output of Cufflinks to complete, sorted and standardised gff3 format.However it occurs" the input file like this: maybe the input file is not in the format agat_sp_gxf_to_gff3.pl can perform.

Juke34 commented 4 years ago

Could you show the full output from the tool? And what is your command? It looks like the path you provide to the file is wrong (--gff option)

wuxiaopei0509 commented 4 years ago

my command id 'agat_sp_gxf_to_gff3.pl -g ./transcripts.gff3 -o out.gff' and no output of agat_sp_gxf_to_gff3.pl, only the error message "=> parse option and metadata: Accessing the feature level files: Using standard /share/features_level1.json file Can't open $file_path": No such file or directory"

Juke34 commented 4 years ago

You should have an header telling the version in use, because the version 0.0.1 was a pre-released. So it could be bugged. But version 0.0.3 should be fine. Did you install using Conda? And the error should specify a specific line...

wuxiaopei0509 commented 4 years ago

Yeah，I install through conda the version is Version: v0.0.3 I work on Linux. the inputfile I use for the script can be found at the attachment transcripts.zip

Juke34 commented 4 years ago

Is not related to your input file. The tool needs parameters stored in json files .... it doesn't succeed to reach them. I don't get how you endup with this path /share/features_level1.json while it should be something like that when installed with Conda /anaconda3/envs/agat_conda/lib/site_perl/5.26.2/auto/share/dist/AGAT/features_level1.json. Maybe you first tried to install yourself using Makefile.PL?

Juke34 commented 4 years ago

Maybe something was wrong in the conda env you have installed it. Try in a new fresh env:

conda create -n agat
conda activate agat
conda --install -c bioconda agat
agat_sp_gxf_to_gff3.pl -g ./transcripts.gff3 -o out.gff

wuxiaopei0509 commented 4 years ago

I install agat as you described above.However I find there is no share directory in /lib/site_perl/5.26.2/auto .

Juke34 commented 4 years ago

I don't understand how is it possible your conda installation is broken.
A work around is to git clone the repository and copy past all json files from the share folder into the folder you want to run the scripts. Ohterwise you could try to install the tool yourself in the agat env (because it has already all the prerequisites) by cloning the repository, move into it, and run

perl Makefile.PL
make
make test
make install

Probably at one of this step you will have an Error/Warning message that tell what is the problem, otherwise the installation should be successfull.

wuxiaopei0509 commented 4 years ago

Thank you .I will try it and reply

wuxiaopei0509 commented 4 years ago

I find the problem.the File::ShareDir::Install module didnot be existed on my system

Juke34 commented 4 years ago

Make sense actually now.
Ok then the conda recipe has to be improve in some way. Thank you very much for your feedback.

Juke34 commented 4 years ago

Should be fixed now. I updated the conda recipe

wuxiaopei0509 commented 4 years ago

Sorry, the module installed and the program cannot work well at last unfortunately。I install agat again by conda and encounter the same problem,the features_level1.json also in the /lib/site_perl/5.26.2/auto/share/dist/AGAT/features_level1.json directory. -- | --

Juke34 commented 4 years ago

did you install agat 0.0.3 build pl526r35_1? Could you give the output of the following commands: which perl conda env list which agat_gxf_to_gff3.pl

wuxiaopei0509 commented 4 years ago

which perl ~/miniconda2/envs/agat/bin/perl

conda env list

# conda environments:
#
base                     /home/wuxiaopei/miniconda2
LTR_retriever            /home/wuxiaopei/miniconda2/envs/LTR_retriever
RMBlast                  /home/wuxiaopei/miniconda2/envs/RMBlast
RepeatMasker             /home/wuxiaopei/miniconda2/envs/RepeatMasker
RepeatModeler            /home/wuxiaopei/miniconda2/envs/RepeatModeler
TRF                      /home/wuxiaopei/miniconda2/envs/TRF
agat                  *  /home/wuxiaopei/miniconda2/envs/agat
augustus                 /home/wuxiaopei/miniconda2/envs/augustus
bioawk                   /home/wuxiaopei/miniconda2/envs/bioawk
blasr                    /home/wuxiaopei/miniconda2/envs/blasr
braker2                  /home/wuxiaopei/miniconda2/envs/braker2
gaas                     /home/wuxiaopei/miniconda2/envs/gaas
mmseqs2                  /home/wuxiaopei/miniconda2/envs/mmseqs2
pb-assembly0.0.3         /home/wuxiaopei/miniconda2/envs/pb-assembly0.0.3
perl5.26                 /home/wuxiaopei/miniconda2/envs/perl5.26
python=3.4               /home/wuxiaopei/miniconda2/envs/python=3.4
seqkit                   /home/wuxiaopei/miniconda2/envs/seqkit
sra-tools                /home/wuxiaopei/miniconda2/envs/sra-tools

which agat_gxf_to_gff3.pl /usr/bin/which: no agat_gxf_to_gff3.pl in ......

by the way, what's the 'build pl526r35_1' mean?

Juke34 commented 4 years ago

oups sorry I meant agat_sp_gxf_to_gff3.pl not agat_gxf_to_gff3.pl and perl --version

wuxiaopei0509 commented 4 years ago

yes ,agat_gxf_to_gff3.pl in the agat environment bin directory

Juke34 commented 4 years ago

I have modified the conda recipe to include File::ShareDir::Install if missing, and it is in the build pl526r35_1 (it is incremented every time we modify the recipe)

wuxiaopei0509 commented 4 years ago

ok,thank you. I will try conda again.

wuxiaopei0509 commented 4 years ago

This script is being run by perl v5.26.2, Bioperl location being used: /home/wuxiaopei/miniconda2/envs/agat/lib/site_perl/5.26.2/Bio/, => parse option and metadata: Accessing the feature level files: Using standard /share/features_level1.json file Can't open $file_path": No such file or directory

also have the problem, what do you mean build pl526r35_1 and where does it locate? thanks

Juke34 commented 4 years ago

When you do conda install agatyou should see

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    agat-0.0.3                 |       pl526r35_1         197 KB  bioconda
    certifi-2019.11.28         |           py37_0         148 KB  conda-forge
    llvm-openmp-8.0.1          |       h770b8ee_0         253 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         598 KB

Here the installed build is specified

Juke34 commented 4 years ago

The json file should be located here /home/wuxiaopei/miniconda2/envs/agat/lib/site_perl/5.26.2/auto/share/dist/AGAT/ A work around would be to copy yourself the files of the AGAT share folder from GitHub into "/share/" folder of your computer because apparently it is looking there.
A second work around would be to copy the same json files into the folder you run AGAT's tools. (The only thing in that that AGAT will not check the feature types against the ontology but it is not problematic).

Btw I'm not sure you will get any interesting statistic against a file containing match match_part feature type (3rd column).

Juke34 commented 4 years ago

Could you copy past this command too conda list? Maybe it is related to a version of perl File::Share module...

wuxiaopei0509 commented 4 years ago

It is very kind of you. First ,The json files are indeed located in /home/wuxiaopei/miniconda2/envs/agat/lib/site_perl/5.26.2/auto/share/dist/AGAT/

I did as you said about the second work , copy the json files and sofa_2_5_3.obo into the folder I run AGAT's tools,the json file work ok, however sofa_2_5_3.obo isn't correct.the error message is

=> parse option and metadata:
   Accessing the feature level files:
      Using local features_level1.json file
      Using local features_level2.json file
      Using local features_level3.json file
      Using local features_spread.json file
   merge_locus option deactivated
   Accessing Ontology
      No ontology accessible from gff file header
      We will use the SOFA ontology distributed with AGAT: /share/sofa_2_5_3.obo
error: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/share/sofa_2_5_3.obo': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/wuxiaopei/miniconda2/envs/agat/lib/site_perl/5.26.2/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /home/wuxiaopei/miniconda2/envs/agat/lib/site_perl/5.26.2/Bio/Root/IO.pm:268
STACK: Bio::OntologyIO::_initialize /home/wuxiaopei/miniconda2/envs/agat/lib/site_perl/5.26.2/Bio/OntologyIO.pm:213
STACK: Bio::OntologyIO::obo::_initialize /home/wuxiaopei/miniconda2/envs/agat/lib/site_perl/5.26.2/Bio/OntologyIO/obo.pm:161
STACK: Bio::OntologyIO::new /home/wuxiaopei/miniconda2/envs/agat/lib/site_perl/5.26.2/Bio/OntologyIO.pm:174
STACK: Bio::OntologyIO::new /home/wuxiaopei/miniconda2/envs/agat/lib/site_perl/5.26.2/Bio/OntologyIO.pm:183
STACK: AGAT::OmniscientI::try {...}  /home/wuxiaopei/perl5/lib/perl5/AGAT/OmniscientI.pm:3090
STACK: Try::Tiny::try /home/wuxiaopei/miniconda2/envs/agat/lib/site_perl/5.26.2/Try/Tiny.pm:102
STACK: AGAT::OmniscientI::_handle_ontology /home/wuxiaopei/perl5/lib/perl5/AGAT/OmniscientI.pm:3115
STACK: AGAT::OmniscientI::slurp_gff3_file_JD /home/wuxiaopei/perl5/lib/perl5/AGAT/OmniscientI.pm:140
STACK: /home/wuxiaopei/miniconda2/envs/agat/bin/agat_sp_gxf_to_gff3.pl:83

I haven't try the first method you suggested,since I am not root,and I don't know how to put share file into my system.

At last.I just want to use the script the statistics the genemodels information about the prediction results provided by Cufflinks and Pasa assembly

Thanks!

Juke34 commented 4 years ago

I thought I had let the possibility to work without ontology, but apparently not. I could modify that for a future version. If your files are well located here: /home/wuxiaopei/miniconda2/envs/agat/lib/site_perl/5.26.2/auto/share/dist/AGAT/then it means the problem is from the module called File::Share.

Here what I have in my conda env

perl-file-share           0.25                    pl526_2    bioconda
perl-file-sharedir        1.116                   pl526_1    bioconda
perl-file-sharedir-install 0.13                    pl526_0    bioconda

Maybe you have a version of perl-file-share that is not working. You can try to install those 3 modules like me to be in the same condition. but only perl-file-share should matter.

wuxiaopei0509 commented 4 years ago

My conda list also have the three module perl-file-share 0.25 pl526_2 bioconda perl-file-sharedir 1.116 pl526_1 bioconda perl-file-sharedir-install 0.13 pl526_0 bioconda

Juke34 commented 4 years ago

A last thing we could try: change the line 13: use File::Share ':all'; by use File::ShareDir ':ALL'; into the file /home/wuxiaopei/miniconda2/envs/agat/lib/site_perl/5.26.2/AGAT/OmniscientI.pm

Both work for me. File::Share is an extension of File::ShareDir maybe there is a bug in File::Share... it would be nice to know

wuxiaopei0509 commented 4 years ago

Sorry ,also doesn't work,maybe be related with my system. I will consider it about after for a while

Juke34 commented 4 years ago

Hi, Could you tell what is your operating system? It might help if we encounter again the problem.

You can anyway use the tool in three ways: 1) As you started to do by copying pasting the json files locally. It was just missing the ontology that is not read in the local folder. You can provide it using an URL in the gtf/gff file header: ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/subsets/SOFA.obo 2) using the container 3) By using the previous script in GAAS

wuxiaopei0509 commented 4 years ago

my operating system is Linux version 2.6.32-431.el6.x86_64(mockbuild@c6b8.bsys.dev.centos.org) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC) )

Juke34 commented 4 years ago

I moved the question related to the output in another thread => #5 for clarity

devonorourke commented 4 years ago

I'm getting this exact error.

"$AGATDIR"/agat_sp_gxf_to_gff3.pl --gff input.gff -o output.gff
-------------------------------------------------------------------------------
This script is being run by perl v5.26.2
Bioperl location being used: /scratch/dro49/conda/envs/agatenv/lib/site_perl/5.26.2/Bio/
-------------------------------------------------------------------------------
=> parse option and metadata:
     Accessing the feature level files:
            Using standard /share/features_level1.json file
load_json: Can't open /share/features_level1.json: No such file or directory

I installed via conda, per the instructions. I did this at 02:00 UTC, Tuesday April 7, 2020.

conda create -n agat
conda activate agat
conda --install -c bioconda agat

Conda list installed the relevant share Perl modules:

perl-file-listing         6.04                    pl526_1    bioconda
perl-file-path            2.16                    pl526_0    bioconda
perl-file-share           0.25                    pl526_2    bioconda
perl-file-sharedir        1.116                   pl526_1    bioconda
perl-file-sharedir-install 0.13                    pl526_0    bioconda
perl-file-slurp-tiny      0.004                   pl526_1    bioconda
perl-file-sort            1.01                    pl526_2    bioconda
perl-file-temp            0.2304                  pl526_2    bioconda
perl-file-which           1.23                    pl526_0    bioconda

I'm running Perl v5.26.2 and am pointing Perl libraries to the AGAT section:

echo $PERL5LIB
/scratch/dro49/conda/envs/agatenv/lib/site_perl/5.26.2

I've tried the line 13 switch you suggested, modifying it to: use File::ShareDir ':ALL';. Same error.

I also tried to add the particular path to the File Perl module to the PERL5LIB variable, but that didn't resolve the issue either.

export PERL5LIB=/scratch/dro49/conda/envs/agatenv/lib/site_perl/5.26.2:/scratch/dro49/conda/envs/agatenv/lib/site_perl/5.26.2/File

Same error.

Finally, I tried modifying the shebang in the OmniscientI.pm script to point to /usr/bin/env perl -w instead of /usr/bin/perl. Same error.

Any ideas? Thank you

Juke34 commented 4 years ago

Hi,

sorry to hear you have this problem too. You are the third person reporting this issue, but I 'm not able to reproduce it. I will see if I can hardcode something to trap this and try in a different way. The fix for now in your case is:

either to copy yourself the files from AGAT/share/* into /share folder of your computer,
or into the working directory (within the folder you plan to run AGAT's scripts ).

devonorourke commented 4 years ago

Hi, Thank you for your help.

I don't think that I'll be able to add the necessary contents to /share on our cluster, as they likely would need sudo access (which I do not have).

I tried try it again after copying the contents in .../AGAT/share into the working directory as you suggested and the program failed with the same message.

Perhaps I could set up a bash alias for "share" to point to a different path than /share ?

Cheers

On Tue, Apr 7, 2020, 3:26 AM Jacques Dainat notifications@github.com wrote:

Hi,

sorry to hear you have this problem too. You are the third person reporting this issue, but I 'm not able to reproduce it. I will see if I can hardcode something to trap this and try in a different way. The fix for now in your case is:

either to copy yourself the files from AGAT/share/* https://github.com/NBISweden/AGAT/tree/master/share into /share folder of your computer,

or into the working directory (within the folder you plan to run AGAT's scripts ).

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/NBISweden/AGAT/issues/4#issuecomment-610223193, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACVKAXBKKXXAJG3ZXALA3Y3RLLITFANCNFSM4JSGKYAQ .

Juke34 commented 4 years ago

Could you try with this version, I added verbosity:

git clone -b sharedir https://github.com/NBISweden/AGAT.git
cd AGAT
perl Makefile.PL
make
make install
agat_sp_gxf_to_gff3.pl --gff t/scripts_output/1.gff -o throw -v 3

devonorourke commented 4 years ago

Test worked, however I needed to change something in your instructions.

git clone worked fine
perl Makefile.PL failed because I didn't have the required Perl modules installed locally, and I wasn't sure where to find potentially globally available Per modules on our cluster where I'm installing this software.

While I don't have a local Perl module file directory on our cluster and haven't set up any method to download Perl modules from CPAN, I noticed that this git clone method came with a Conda .yml file and created an AGAT Conda environment following that instruction.

Thus, after a failed perl Makefile.PL command, I created an AGAT environment, activated that environment, and followed the remaining steps:
```
conda env create -f conda_environment_AGAT.yml
conda activate agat
perl Makefile.PL
make
make install
```
The command you supplied worked correctly thereafter.

I've tested this with my own files and it appears to be working also.

From what I can tell, my previous failed attempt created an environment using just the bioconda channel. In contrast, the .yml method generated a list of three channels to derive Conda packages from. Maybe something is different between these two methods?

failed way

conda create -n agat
conda activate agat
conda --install -c bioconda agat

successful way

git clone -b sharedir https://github.com/NBISweden/AGAT.git
cd AGAT
conda env create -f conda_environment_AGAT.yml
conda activate agat

Thanks for your attention, support, and development of this software.

Cheers

Juke34 commented 4 years ago

Sorry I forgot to mention to be in the agat Conda environment (the first one you called agatenv) before to perform the commands. It is good that it works and you found your way.

Now I'm wondering if it is related to the new Conda env or to the few changes I have done in the code. Could you give a try (re-do all the commands) within the previous env? Or similarly you can remove the agat env you have created with the conda_environment_AGAT.yml file and re-do all the command except to use the modified code git clone -b sharedir https://github.com/NBISweden/AGAT.git use the original one git clone https://github.com/NBISweden/AGAT.git

devonorourke commented 4 years ago

Just deleted the working AGAT virtual environment (agat); the older virtual environment that failed to work initially was also removed prior to that (agatenv). I also deleted the cloned directory AGAT. Thus I was starting from scratch.

I then installed AGAT via git using the Conda .yml file as follows:

git clone https://github.com/NBISweden/AGAT.git
cd AGAT/
conda env create -f conda_environment_AGAT.yml
conda activate agat

Unfortunately, while installation of AGAT was successful, applying any scripts from the activated environment do not appear to work. Two things I noticed:

If I don't specify the full path to an AGAT .pl script, and instead just write only the name of the program, it is not recognized in my activated Conda $PATH. The necessary PATH to the environment appears to be there, however:
```
echo $PATH
/scratch/dro49/conda/envs/agat/bin:/packages/python/anaconda3/2020.02/bin
```

When things were working properly yesterday, I didn't need to specify the full path to get the .pl scripts to run. So something like this would work from any directory on my machine:

agat_sp_add_start_and_stop.pl \
--gff myBroken.gff \
--fasta myAmazing.fa \
--out myFixed.gff

Now, that just produces an error if I submit it via our Slurm job manager on our cluster:

/var/spool/slurm/slurmd/job29403582/slurm_script: line 14: agat_sp_add_start_and_stop.pl: command not found

or, just says that the script can't be found if you're not in the proper directory:

-bash: agat_sp_add_start_and_stop.pl: command not found

If I do specify the proper path to the directory where the relevant AGAT .pl script is located, it also doesn't work, though, gives a more specific error. This happens whether I'm running this program from a Slurm submission script to our cluster or just try something on the head node:

Possible precedence issue with control flow operator at /scratch/dro49/conda/envs/funenv/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Can't locate AGAT/Omniscient.pm in @INC (you may need to install the AGAT::Omniscient module) (@INC contains: /lib/site_perl /scratch/dro49/conda/envs/agat/lib/site_perl/5.26.2/x86_64-linux-thread-multi /scratch/dro49/conda/envs/agat/lib/site_perl/5.26.2 /scratch/dro49/conda/envs/agat/lib/5.26.2/x86_64-linux-thread-multi /scratch/dro49/conda/envs/agat/lib/5.26.2 .) at ./agat_sp_add_start_and_stop.pl line 13.
BEGIN failed--compilation aborted at ./agat_sp_add_start_and_stop.pl line 13.

I believe this points to something you did in the code as being important?

Juke34 commented 4 years ago

doing that is not sufficient:

git clone https://github.com/NBISweden/AGAT.git
cd AGAT/
conda env create -f conda_environment_AGAT.yml
conda activate agat

it just installs the dependencies (perl, R,etc...). It does not install AGAT. To perform the AGAT installation from the local clone of the repo you should then do

perl Makefile.PL
make
make install

This will put the scripts and modules where it should be in the env.

devonorourke commented 4 years ago

Ouch. Sorry about that. After running those three additional lines everything worked properly. No errors to report.

Juke34 commented 4 years ago

Then the error is indeed related to one of the dependencies... Could you do conda list and copy past the result? Then do

conda create -n agat2
conda activate agat2
conda install -c bioconda agat

Test this installation (it should fails). then do conda list and copy past the result. This is the only way to see the differences

devonorourke commented 4 years ago

agat Conda list output:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
binutils_impl_linux-64    2.34                 h53a641e_0    conda-forge
binutils_linux-64         2.34                hc952b39_18    conda-forge
bwidget                   1.9.14                        0    conda-forge
bzip2                     1.0.8                h516909a_2    conda-forge
ca-certificates           2020.4.5.1           hecc5488_0    conda-forge
cairo                     1.16.0            hcf35c78_1003    conda-forge
certifi                   2020.4.5.1       py37hc8dfbb8_0    conda-forge
clustalw                  2.1                  hc9558a2_5    bioconda
curl                      7.68.0               hf8cf82a_0    conda-forge
expat                     2.2.9                he1b5a44_2    conda-forge
fontconfig                2.13.1            h86ecdb6_1001    conda-forge
freetype                  2.10.1               he06d7ca_0    conda-forge
fribidi                   1.0.9                h516909a_0    conda-forge
gcc_impl_linux-64         7.3.0                hd420e75_5    conda-forge
gcc_linux-64              7.3.0               h553295d_18    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
gfortran_impl_linux-64    7.3.0                hdf63c60_5    conda-forge
gfortran_linux-64         7.3.0               h553295d_18    conda-forge
giflib                    5.2.1                h516909a_2    conda-forge
glib                      2.58.3          py37he00f558_1003    conda-forge
graphite2                 1.3.13            he1b5a44_1001    conda-forge
graphviz                  2.42.3               h0511662_0    conda-forge
gsl                       2.5                  h294904e_1    conda-forge
gxx_impl_linux-64         7.3.0                hdf63c60_5    conda-forge
gxx_linux-64              7.3.0               h553295d_18    conda-forge
harfbuzz                  2.4.0                h9f30f68_3    conda-forge
icu                       64.2                 he1b5a44_1    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
krb5                      1.16.4               h2fd8d38_0    conda-forge
ld_impl_linux-64          2.34                 h53a641e_0    conda-forge
libblas                   3.8.0               16_openblas    conda-forge
libcblas                  3.8.0               16_openblas    conda-forge
libcurl                   7.68.0               hda55be3_0    conda-forge
libdb                     6.1.26            he1b5a44_2001    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgd                     2.2.5             h307a58e_1007    conda-forge
libgfortran-ng            7.3.0                hdf63c60_5    conda-forge
libgomp                   9.2.0                h24d8f2e_2    conda-forge
libiconv                  1.15              h516909a_1006    conda-forge
libopenblas               0.3.9                h5ec1e0e_0    conda-forge
libpng                    1.6.37               hed695b0_1    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
libtiff                   4.1.0                hc3755c2_3    conda-forge
libtool                   2.4.6             h14c3975_1002    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp                   1.0.2                h56121f0_5    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.10               hee79883_0    conda-forge
libxslt                   1.1.33               h31b3aaa_0    conda-forge
llvm-openmp               9.0.1                hc9558a2_2    conda-forge
lz4-c                     1.8.3             he1b5a44_1001    conda-forge
make                      4.3                  h516909a_0    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
openssl                   1.1.1f               h516909a_0    conda-forge
paml                      4.9                  h516909a_5    bioconda
pango                     1.42.4               h7062337_4    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
perl                      5.26.2            h516909a_1006    conda-forge
perl-aceperl              1.92                    pl526_2    bioconda
perl-algorithm-diff       1.1903                  pl526_2    bioconda
perl-algorithm-munkres    0.08                    pl526_1    bioconda
perl-apache-test          1.40                    pl526_1    bioconda
perl-app-cpanminus        1.7044                  pl526_1    bioconda
perl-appconfig            1.71                    pl526_1    bioconda
perl-array-compare        3.0.1                   pl526_1    bioconda
perl-autoloader           5.74                    pl526_2    bioconda
perl-base                 2.23                    pl526_1    bioconda
perl-bio-asn1-entrezgene  1.73                    pl526_1    bioconda
perl-bio-coordinate       1.007001                pl526_1    bioconda
perl-bio-featureio        1.6.905                 pl526_2    bioconda
perl-bio-phylo            0.58                    pl526_2    bioconda
perl-bio-samtools         1.43            pl526h1341992_1    bioconda
perl-bio-tools-phylo-paml 1.7.3                   pl526_1    bioconda
perl-bio-tools-run-alignment-clustalw 1.7.4                   pl526_1    bioconda
perl-bio-tools-run-alignment-tcoffee 1.7.4                   pl526_2    bioconda
perl-bioperl              1.7.2                  pl526_11    bioconda
perl-bioperl-core         1.007002                pl526_2    bioconda
perl-bioperl-run          1.007002                pl526_4    bioconda
perl-business-isbn        3.004                   pl526_0    bioconda
perl-business-isbn-data   20140910.003            pl526_0    bioconda
perl-cache-cache          1.08                    pl526_0    bioconda
perl-capture-tiny         0.48                    pl526_0    bioconda
perl-carp                 1.38                    pl526_3    bioconda
perl-cgi                  4.44            pl526h14c3975_1    bioconda
perl-class-data-inheritable 0.08                    pl526_1    bioconda
perl-class-inspector      1.34                    pl526_0    bioconda
perl-class-load           0.25                    pl526_0    bioconda
perl-class-load-xs        0.10            pl526h6bb024c_2    bioconda
perl-class-method-modifiers 2.12                    pl526_0    bioconda
perl-clone                0.42            pl526h516909a_0    bioconda
perl-common-sense         3.74                    pl526_2    bioconda
perl-compress-raw-zlib    2.087           pl526hc9558a2_0    bioconda
perl-constant             1.33                    pl526_1    bioconda
perl-convert-binary-c     0.78            pl526h6bb024c_3    bioconda
perl-convert-binhex       1.125                   pl526_1    bioconda
perl-crypt-rc4            2.02                    pl526_1    bioconda
perl-data-dumper          2.173                   pl526_0    bioconda
perl-data-optlist         0.110                   pl526_2    bioconda
perl-data-stag            0.14                    pl526_1    bioconda
perl-date-format          2.30                    pl526_2    bioconda
perl-db-file              1.852           pl526h14c3975_0    bioconda
perl-dbd-sqlite           1.64            pl526h516909a_0    bioconda
perl-dbi                  1.642                   pl526_0    bioconda
perl-devel-globaldestruction 0.14                    pl526_0    bioconda
perl-devel-overloadinfo   0.005                   pl526_0    bioconda
perl-devel-stacktrace     2.04                    pl526_0    bioconda
perl-digest-hmac          1.03                    pl526_3    bioconda
perl-digest-md5           2.55                    pl526_0    bioconda
perl-digest-perl-md5      1.9                     pl526_1    bioconda
perl-digest-sha1          2.13            pl526h6bb024c_1    bioconda
perl-dist-checkconflicts  0.11                    pl526_2    bioconda
perl-dynaloader           1.25                    pl526_1    bioconda
perl-email-date-format    1.005                   pl526_2    bioconda
perl-encode               2.88                    pl526_1    bioconda
perl-encode-locale        1.05                    pl526_6    bioconda
perl-error                0.17027                 pl526_1    bioconda
perl-eval-closure         0.14            pl526h6bb024c_4    bioconda
perl-exception-class      1.44                    pl526_0    bioconda
perl-exporter             5.72                    pl526_1    bioconda
perl-exporter-tiny        1.002001                pl526_0    bioconda
perl-extutils-makemaker   7.36                    pl526_1    bioconda
perl-file-listing         6.04                    pl526_1    bioconda
perl-file-path            2.16                    pl526_0    bioconda
perl-file-share           0.25                    pl526_2    bioconda
perl-file-sharedir        1.116                   pl526_1    bioconda
perl-file-sharedir-install 0.13                    pl526_0    bioconda
perl-file-slurp-tiny      0.004                   pl526_1    bioconda
perl-file-sort            1.01                    pl526_2    bioconda
perl-file-temp            0.2304                  pl526_2    bioconda
perl-file-which           1.23                    pl526_0    bioconda
perl-font-afm             1.20                    pl526_2    bioconda
perl-font-ttf             1.06                    pl526_0    bioconda
perl-gd                   2.71            pl526he860b03_0    bioconda
perl-getopt-long          2.50                    pl526_1    bioconda
perl-graph                0.9704                  pl526_1    bioconda
perl-graphviz             2.24            pl526h734ff71_0    bioconda
perl-html-element-extended 1.18                    pl526_1    bioconda
perl-html-entities-numbered 0.04                    pl526_1    bioconda
perl-html-formatter       2.16                    pl526_0    bioconda
perl-html-parser          3.72            pl526h6bb024c_5    bioconda
perl-html-tableextract    2.13                    pl526_2    bioconda
perl-html-tagset          3.20                    pl526_3    bioconda
perl-html-tidy            1.60                    pl526_0    bioconda
perl-html-tree            5.07                    pl526_1    bioconda
perl-html-treebuilder-xpath 0.14                    pl526_1    bioconda
perl-http-cookies         6.04                    pl526_0    bioconda
perl-http-daemon          6.01                    pl526_1    bioconda
perl-http-date            6.02                    pl526_3    bioconda
perl-http-message         6.18                    pl526_0    bioconda
perl-http-negotiate       6.01                    pl526_3    bioconda
perl-image-info           1.38                    pl526_1    bioconda
perl-image-size           3.300                   pl526_2    bioconda
perl-io-html              1.001                   pl526_2    bioconda
perl-io-sessiondata       1.03                    pl526_1    bioconda
perl-io-socket-ssl        2.066                   pl526_0    bioconda
perl-io-string            1.08                    pl526_3    bioconda
perl-io-stringy           2.111                   pl526_1    bioconda
perl-io-tty               1.12                    pl526_1    bioconda
perl-ipc-run              20180523.0              pl526_0    bioconda
perl-ipc-sharelite        0.17            pl526h6bb024c_1    bioconda
perl-jcode                2.07                    pl526_2    bioconda
perl-json                 4.02                    pl526_0    bioconda
perl-json-xs              2.34            pl526h6bb024c_3    bioconda
perl-lib                  0.63                    pl526_1    bioconda
perl-libwww-perl          6.39                    pl526_0    bioconda
perl-libxml-perl          0.08                    pl526_2    bioconda
perl-list-moreutils       0.428                   pl526_1    bioconda
perl-list-moreutils-xs    0.428                   pl526_0    bioconda
perl-lwp-mediatypes       6.04                    pl526_0    bioconda
perl-lwp-protocol-https   6.07                    pl526_4    bioconda
perl-lwp-simple           6.15            pl526h470a237_4    bioconda
perl-mailtools            2.21                    pl526_0    bioconda
perl-math-cdf             0.1             pl526h14c3975_5    bioconda
perl-math-derivative      1.01                    pl526_0    bioconda
perl-math-random          0.72            pl526h14c3975_2    bioconda
perl-math-spline          0.02                    pl526_2    bioconda
perl-mime-base64          3.15                    pl526_1    bioconda
perl-mime-lite            3.030                   pl526_1    bioconda
perl-mime-tools           5.508                   pl526_1    bioconda
perl-mime-types           2.17                    pl526_0    bioconda
perl-mldbm                2.05                    pl526_1    bioconda
perl-module-implementation 0.09                    pl526_2    bioconda
perl-module-runtime       0.016                   pl526_1    bioconda
perl-module-runtime-conflicts 0.003                   pl526_0    bioconda
perl-moo                  2.003004                pl526_0    bioconda
perl-moose                2.2011          pl526hf484d3e_1    bioconda
perl-mozilla-ca           20180117                pl526_1    bioconda
perl-mro-compat           0.13                    pl526_0    bioconda
perl-net-http             6.19                    pl526_0    bioconda
perl-net-ssleay           1.88            pl526h90d6eec_0    bioconda
perl-ntlm                 1.09                    pl526_4    bioconda
perl-ole-storage_lite     0.19                    pl526_3    bioconda
perl-package-deprecationmanager 0.17                    pl526_0    bioconda
perl-package-stash        0.38            pl526hf484d3e_1    bioconda
perl-package-stash-xs     0.28            pl526hf484d3e_1    bioconda
perl-params-util          1.07            pl526h6bb024c_4    bioconda
perl-parent               0.236                   pl526_1    bioconda
perl-parse-recdescent     1.967015                pl526_0    bioconda
perl-pathtools            3.75            pl526h14c3975_1    bioconda
perl-pdf-api2             2.035                   pl526_0    bioconda
perl-pod-escapes          1.07                    pl526_1    bioconda
perl-pod-usage            1.69                    pl526_1    bioconda
perl-postscript           0.06                    pl526_2    bioconda
perl-regexp-common        2017060201              pl526_0    bioconda
perl-role-tiny            2.000008                pl526_0    bioconda
perl-scalar-list-utils    1.52            pl526h516909a_0    bioconda
perl-set-scalar           1.29                    pl526_2    bioconda
perl-soap-lite            1.19                    pl526_1    bioconda
perl-socket               2.027                   pl526_1    bioconda
perl-sort-naturally       1.03                    pl526_2    bioconda
perl-spreadsheet-parseexcel 0.65                    pl526_2    bioconda
perl-spreadsheet-writeexcel 2.40                    pl526_2    bioconda
perl-statistics-descriptive 3.0702                  pl526_0    bioconda
perl-statistics-r         0.34                pl526r351_3    bioconda
perl-storable             3.15            pl526h14c3975_0    bioconda
perl-sub-exporter         0.987                   pl526_2    bioconda
perl-sub-exporter-progressive 0.001013                pl526_0    bioconda
perl-sub-identify         0.14            pl526h14c3975_0    bioconda
perl-sub-install          0.928                   pl526_2    bioconda
perl-sub-name             0.21                    pl526_1    bioconda
perl-sub-quote            2.006003                pl526_1    bioconda
perl-sub-uplevel          0.2800          pl526h14c3975_2    bioconda
perl-svg                  2.84                    pl526_0    bioconda
perl-svg-graph            0.02                    pl526_3    bioconda
perl-task-weaken          1.06                    pl526_0    bioconda
perl-template-toolkit     2.26                    pl526_1    bioconda
perl-test                 1.26                    pl526_1    bioconda
perl-test-deep            1.128                   pl526_1    bioconda
perl-test-differences     0.67                    pl526_0    bioconda
perl-test-exception       0.43                    pl526_2    bioconda
perl-test-harness         3.42                    pl526_0    bioconda
perl-test-leaktrace       0.16            pl526h14c3975_2    bioconda
perl-test-most            0.35                    pl526_0    bioconda
perl-test-requiresinternet 0.05                    pl526_0    bioconda
perl-test-warn            0.36                    pl526_1    bioconda
perl-text-balanced        2.03                    pl526_3    bioconda
perl-text-diff            1.45                    pl526_0    bioconda
perl-text-wrap            2013.0523               pl526_1    bioconda
perl-tie-ixhash           1.23                    pl526_2    bioconda
perl-time-hires           1.9760          pl526h14c3975_1    bioconda
perl-time-local           1.28                    pl526_1    bioconda
perl-timedate             2.30                    pl526_1    bioconda
perl-tree-dag_node        1.31                    pl526_0    bioconda
perl-try-tiny             0.30                    pl526_1    bioconda
perl-type-tiny            1.004004                pl526_0    bioconda
perl-types-serialiser     1.0                     pl526_2    bioconda
perl-unicode-map          0.112           pl526h6bb024c_3    bioconda
perl-uri                  1.76                    pl526_0    bioconda
perl-www-robotrules       6.02                    pl526_3    bioconda
perl-xml-dom              1.46                    pl526_0    bioconda
perl-xml-dom-xpath        0.14                    pl526_1    bioconda
perl-xml-filter-buffertext 1.01                    pl526_2    bioconda
perl-xml-libxml           2.0132          pl526h7ec2d77_1    bioconda
perl-xml-libxslt          1.94                    pl526_1    bioconda
perl-xml-namespacesupport 1.12                    pl526_0    bioconda
perl-xml-parser           2.44_01         pl526ha1d75be_1002    conda-forge
perl-xml-regexp           0.04                    pl526_2    bioconda
perl-xml-sax              1.02                    pl526_0    bioconda
perl-xml-sax-base         1.09                    pl526_0    bioconda
perl-xml-sax-expat        0.51                    pl526_3    bioconda
perl-xml-sax-writer       0.57                    pl526_0    bioconda
perl-xml-simple           2.25                    pl526_1    bioconda
perl-xml-twig             3.52                    pl526_2    bioconda
perl-xml-writer           0.625                   pl526_2    bioconda
perl-xml-xpath            1.44                    pl526_0    bioconda
perl-xml-xpathengine      0.14                    pl526_2    bioconda
perl-xsloader             0.24                    pl526_0    bioconda
perl-yaml                 1.29                    pl526_0    bioconda
pip                       20.0.2                     py_2    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
python                    3.7.6           h8356626_5_cpython    conda-forge
python_abi                3.7                     1_cp37m    conda-forge
r-base                    3.5.1             hc461eb7_1012    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
setuptools                46.1.3           py37hc8dfbb8_0    conda-forge
sqlite                    3.30.1               hcee41ef_0    conda-forge
t_coffee                  11.0.8           py37hea885bf_8    bioconda
tidyp                     1.04                          1    bioconda
tk                        8.6.10               hed695b0_0    conda-forge
tktable                   2.10                 h555a92e_3    conda-forge
wheel                     0.34.2                     py_1    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.9                h516909a_0    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxpm               3.5.13               h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-libxt                1.1.5             h516909a_1003    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.5                h516909a_0    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge
zstd                      1.4.4                h3b9ef0a_2    conda-forge

agat2 installation threw a million ClobberError posts. Here's just a few:

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda/linux-64::perl-package-stash-0.38-pl526hf484d3e_1, bioconda/linux-64::perl-sub-exporter-0.987-pl526_2
  path: 'lib/site_perl/5.26.2/x86_64-linux-thread-multi/auto/Sub/Exporter/.packlist'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda/linux-64::perl-package-stash-0.38-pl526hf484d3e_1, bioconda/linux-64::perl-sub-exporter-0.987-pl526_2
  path: 'man/man3/Sub::Exporter.3'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda/linux-64::perl-package-stash-0.38-pl526hf484d3e_1, bioconda/linux-64::perl-sub-exporter-0.987-pl526_2
  path: 'man/man3/Sub::Exporter::Cookbook.3'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda/linux-64::perl-package-stash-0.38-pl526hf484d3e_1, bioconda/linux-64::perl-sub-exporter-0.987-pl526_2
  path: 'man/man3/Sub::Exporter::Tutorial.3'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: bioconda/linux-64::perl-package-stash-0.38-pl526hf484d3e_1, bioconda/linux-64::perl-sub-exporter-0.987-pl526_2
  path: 'man/man3/Sub::Exporter::Util.3'

However, I can run the .pl scripts in /scratch/dro49/conda/envs/agat2/bin!

Here's the list of Conda files in that environment:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
agat                      0.2.3                pl526r35_0    bioconda
binutils_impl_linux-64    2.34                 h53a641e_0    conda-forge
binutils_linux-64         2.34                hc952b39_18    conda-forge
bwidget                   1.9.14                        0    conda-forge
bzip2                     1.0.8                h516909a_2    conda-forge
ca-certificates           2020.4.5.1           hecc5488_0    conda-forge
cairo                     1.16.0            hcf35c78_1003    conda-forge
certifi                   2020.4.5.1       py37hc8dfbb8_0    conda-forge
clustalw                  2.1                  hc9558a2_5    bioconda
curl                      7.68.0               hf8cf82a_0    conda-forge
expat                     2.2.9                he1b5a44_2    conda-forge
fontconfig                2.13.1            h86ecdb6_1001    conda-forge
freetype                  2.10.1               he06d7ca_0    conda-forge
fribidi                   1.0.9                h516909a_0    conda-forge
gcc_impl_linux-64         7.3.0                hd420e75_5    conda-forge
gcc_linux-64              7.3.0               h553295d_18    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
gfortran_impl_linux-64    7.3.0                hdf63c60_5    conda-forge
gfortran_linux-64         7.3.0               h553295d_18    conda-forge
giflib                    5.2.1                h516909a_2    conda-forge
glib                      2.58.3          py37he00f558_1003    conda-forge
graphite2                 1.3.13            he1b5a44_1001    conda-forge
graphviz                  2.42.3               h0511662_0    conda-forge
gsl                       2.5                  h294904e_1    conda-forge
gxx_impl_linux-64         7.3.0                hdf63c60_5    conda-forge
gxx_linux-64              7.3.0               h553295d_18    conda-forge
harfbuzz                  2.4.0                h9f30f68_3    conda-forge
icu                       64.2                 he1b5a44_1    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
krb5                      1.16.4               h2fd8d38_0    conda-forge
ld_impl_linux-64          2.34                 h53a641e_0    conda-forge
libblas                   3.8.0               16_openblas    conda-forge
libcblas                  3.8.0               16_openblas    conda-forge
libcurl                   7.68.0               hda55be3_0    conda-forge
libdb                     6.1.26                        0    bioconda
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgd                     2.2.5             h307a58e_1007    conda-forge
libgfortran-ng            7.3.0                hdf63c60_5    conda-forge
libgomp                   9.2.0                h24d8f2e_2    conda-forge
libiconv                  1.15              h516909a_1006    conda-forge
libopenblas               0.3.9                h5ec1e0e_0    conda-forge
libpng                    1.6.37               hed695b0_1    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
libtiff                   4.1.0                hc3755c2_3    conda-forge
libtool                   2.4.6             h14c3975_1002    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp                   1.0.2                h56121f0_5    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.10               hee79883_0    conda-forge
libxslt                   1.1.33               h31b3aaa_0    conda-forge
llvm-openmp               9.0.1                hc9558a2_2    conda-forge
lz4-c                     1.8.3             he1b5a44_1001    conda-forge
make                      4.3                  h516909a_0    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
openssl                   1.1.1f               h516909a_0    conda-forge
paml                      4.9                  h516909a_5    bioconda
pango                     1.42.4               h7062337_4    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
perl                      5.26.2            h516909a_1006    conda-forge
perl-aceperl              1.92                    pl526_2    bioconda
perl-algorithm-diff       1.1903                  pl526_2    bioconda
perl-algorithm-munkres    0.08                    pl526_1    bioconda
perl-apache-test          1.40                    pl526_1    bioconda
perl-app-cpanminus        1.7044                  pl526_1    bioconda
perl-appconfig            1.71                    pl526_1    bioconda
perl-array-compare        3.0.1                   pl526_1    bioconda
perl-autoloader           5.74                    pl526_2    bioconda
perl-base                 2.23                    pl526_1    bioconda
perl-bio-asn1-entrezgene  1.73                    pl526_1    bioconda
perl-bio-coordinate       1.007001                pl526_1    bioconda
perl-bio-featureio        1.6.905                 pl526_2    bioconda
perl-bio-phylo            0.58                    pl526_2    bioconda
perl-bio-samtools         1.43            pl526h1341992_1    bioconda
perl-bio-tools-phylo-paml 1.7.3                   pl526_1    bioconda
perl-bio-tools-run-alignment-clustalw 1.7.4                   pl526_1    bioconda
perl-bio-tools-run-alignment-tcoffee 1.7.4                   pl526_2    bioconda
perl-bioperl              1.7.2                  pl526_11    bioconda
perl-bioperl-core         1.007002                pl526_2    bioconda
perl-bioperl-run          1.007002                pl526_4    bioconda
perl-business-isbn        3.004                   pl526_0    bioconda
perl-business-isbn-data   20140910.003            pl526_0    bioconda
perl-cache-cache          1.08                    pl526_0    bioconda
perl-capture-tiny         0.48                    pl526_0    bioconda
perl-carp                 1.38                    pl526_3    bioconda
perl-cgi                  4.44            pl526h14c3975_1    bioconda
perl-class-data-inheritable 0.08                    pl526_1    bioconda
perl-class-inspector      1.34                    pl526_0    bioconda
perl-class-load           0.25                    pl526_0    bioconda
perl-class-load-xs        0.10            pl526h6bb024c_2    bioconda
perl-class-method-modifiers 2.12                    pl526_0    bioconda
perl-clone                0.42            pl526h516909a_0    bioconda
perl-common-sense         3.74                    pl526_2    bioconda
perl-compress-raw-zlib    2.087           pl526hc9558a2_0    bioconda
perl-constant             1.33                    pl526_1    bioconda
perl-convert-binary-c     0.78            pl526h6bb024c_3    bioconda
perl-convert-binhex       1.125                   pl526_1    bioconda
perl-crypt-rc4            2.02                    pl526_1    bioconda
perl-data-dumper          2.173                   pl526_0    bioconda
perl-data-optlist         0.110                   pl526_2    bioconda
perl-data-stag            0.14                    pl526_1    bioconda
perl-date-format          2.30                    pl526_2    bioconda
perl-db-file              1.852           pl526h14c3975_0    bioconda
perl-dbd-sqlite           1.64            pl526h516909a_0    bioconda
perl-dbi                  1.642                   pl526_0    bioconda
perl-devel-globaldestruction 0.14                    pl526_0    bioconda
perl-devel-overloadinfo   0.005                   pl526_0    bioconda
perl-devel-stacktrace     2.04                    pl526_0    bioconda
perl-digest-hmac          1.03                    pl526_3    bioconda
perl-digest-md5           2.55                    pl526_0    bioconda
perl-digest-perl-md5      1.9                     pl526_1    bioconda
perl-digest-sha1          2.13            pl526h6bb024c_1    bioconda
perl-dist-checkconflicts  0.11                    pl526_2    bioconda
perl-dynaloader           1.25                    pl526_1    bioconda
perl-email-date-format    1.005                   pl526_2    bioconda
perl-encode               2.88                    pl526_1    bioconda
perl-encode-locale        1.05                    pl526_6    bioconda
perl-error                0.17027                 pl526_1    bioconda
perl-eval-closure         0.14            pl526h6bb024c_4    bioconda
perl-exception-class      1.44                    pl526_0    bioconda
perl-exporter             5.72                    pl526_1    bioconda
perl-exporter-tiny        1.002001                pl526_0    bioconda
perl-extutils-makemaker   7.36                    pl526_1    bioconda
perl-file-listing         6.04                    pl526_1    bioconda
perl-file-path            2.16                    pl526_0    bioconda
perl-file-share           0.25                    pl526_2    bioconda
perl-file-sharedir        1.116                   pl526_1    bioconda
perl-file-sharedir-install 0.13                    pl526_0    bioconda
perl-file-slurp-tiny      0.004                   pl526_1    bioconda
perl-file-sort            1.01                    pl526_2    bioconda
perl-file-temp            0.2304                  pl526_2    bioconda
perl-file-which           1.23                    pl526_0    bioconda
perl-font-afm             1.20                    pl526_2    bioconda
perl-font-ttf             1.06                    pl526_0    bioconda
perl-gd                   2.71            pl526he860b03_0    bioconda
perl-getopt-long          2.50                    pl526_1    bioconda
perl-graph                0.9704                  pl526_1    bioconda
perl-graphviz             2.24            pl526h734ff71_0    bioconda
perl-html-element-extended 1.18                    pl526_1    bioconda
perl-html-entities-numbered 0.04                    pl526_1    bioconda
perl-html-formatter       2.16                    pl526_0    bioconda
perl-html-parser          3.72            pl526h6bb024c_5    bioconda
perl-html-tableextract    2.13                    pl526_2    bioconda
perl-html-tagset          3.20                    pl526_3    bioconda
perl-html-tidy            1.60                    pl526_0    bioconda
perl-html-tree            5.07                    pl526_1    bioconda
perl-html-treebuilder-xpath 0.14                    pl526_1    bioconda
perl-http-cookies         6.04                    pl526_0    bioconda
perl-http-daemon          6.01                    pl526_1    bioconda
perl-http-date            6.02                    pl526_3    bioconda
perl-http-message         6.18                    pl526_0    bioconda
perl-http-negotiate       6.01                    pl526_3    bioconda
perl-image-info           1.38                    pl526_1    bioconda
perl-image-size           3.300                   pl526_2    bioconda
perl-io-html              1.001                   pl526_2    bioconda
perl-io-sessiondata       1.03                    pl526_1    bioconda
perl-io-socket-ssl        2.066                   pl526_0    bioconda
perl-io-string            1.08                    pl526_3    bioconda
perl-io-stringy           2.111                   pl526_1    bioconda
perl-io-tty               1.12                    pl526_1    bioconda
perl-ipc-run              20180523.0              pl526_0    bioconda
perl-ipc-sharelite        0.17            pl526h6bb024c_1    bioconda
perl-jcode                2.07                    pl526_2    bioconda
perl-json                 4.02                    pl526_0    bioconda
perl-json-xs              2.34            pl526h6bb024c_3    bioconda
perl-lib                  0.63                    pl526_1    bioconda
perl-libwww-perl          6.39                    pl526_0    bioconda
perl-libxml-perl          0.08                    pl526_2    bioconda
perl-list-moreutils       0.428                   pl526_1    bioconda
perl-list-moreutils-xs    0.428                   pl526_0    bioconda
perl-lwp-mediatypes       6.04                    pl526_0    bioconda
perl-lwp-protocol-https   6.07                    pl526_4    bioconda
perl-lwp-simple           6.15            pl526h470a237_4    bioconda
perl-mailtools            2.21                    pl526_0    bioconda
perl-math-cdf             0.1             pl526h14c3975_5    bioconda
perl-math-derivative      1.01                    pl526_0    bioconda
perl-math-random          0.72            pl526h14c3975_2    bioconda
perl-math-spline          0.02                    pl526_2    bioconda
perl-mime-base64          3.15                    pl526_1    bioconda
perl-mime-lite            3.030                   pl526_1    bioconda
perl-mime-tools           5.508                   pl526_1    bioconda
perl-mime-types           2.17                    pl526_0    bioconda
perl-mldbm                2.05                    pl526_1    bioconda
perl-module-implementation 0.09                    pl526_2    bioconda
perl-module-runtime       0.016                   pl526_1    bioconda
perl-module-runtime-conflicts 0.003                   pl526_0    bioconda
perl-moo                  2.003004                pl526_0    bioconda
perl-moose                2.2011          pl526hf484d3e_1    bioconda
perl-mozilla-ca           20180117                pl526_1    bioconda
perl-mro-compat           0.13                    pl526_0    bioconda
perl-net-http             6.19                    pl526_0    bioconda
perl-net-ssleay           1.88            pl526h90d6eec_0    bioconda
perl-ntlm                 1.09                    pl526_4    bioconda
perl-ole-storage_lite     0.19                    pl526_3    bioconda
perl-package-deprecationmanager 0.17                    pl526_0    bioconda
perl-package-stash        0.38            pl526hf484d3e_1    bioconda
perl-package-stash-xs     0.28            pl526hf484d3e_1    bioconda
perl-params-util          1.07            pl526h6bb024c_4    bioconda
perl-parent               0.236                   pl526_1    bioconda
perl-parse-recdescent     1.967015                pl526_0    bioconda
perl-pathtools            3.75            pl526h14c3975_1    bioconda
perl-pdf-api2             2.035                   pl526_0    bioconda
perl-pod-escapes          1.07                    pl526_1    bioconda
perl-pod-usage            1.69                    pl526_1    bioconda
perl-postscript           0.06                    pl526_2    bioconda
perl-regexp-common        2017060201              pl526_0    bioconda
perl-role-tiny            2.000008                pl526_0    bioconda
perl-scalar-list-utils    1.52            pl526h516909a_0    bioconda
perl-set-scalar           1.29                    pl526_2    bioconda
perl-soap-lite            1.19                    pl526_1    bioconda
perl-socket               2.027                   pl526_1    bioconda
perl-sort-naturally       1.03                    pl526_2    bioconda
perl-spreadsheet-parseexcel 0.65                    pl526_2    bioconda
perl-spreadsheet-writeexcel 2.40                    pl526_2    bioconda
perl-statistics-descriptive 3.0702                  pl526_0    bioconda
perl-statistics-r         0.34                pl526r351_3    bioconda
perl-storable             3.15            pl526h14c3975_0    bioconda
perl-sub-exporter         0.987                   pl526_2    bioconda
perl-sub-exporter-progressive 0.001013                pl526_0    bioconda
perl-sub-identify         0.14            pl526h14c3975_0    bioconda
perl-sub-install          0.928                   pl526_2    bioconda
perl-sub-name             0.21                    pl526_1    bioconda
perl-sub-quote            2.006003                pl526_1    bioconda
perl-sub-uplevel          0.2800          pl526h14c3975_2    bioconda
perl-svg                  2.84                    pl526_0    bioconda
perl-svg-graph            0.02                    pl526_3    bioconda
perl-task-weaken          1.06                    pl526_0    bioconda
perl-template-toolkit     2.26                    pl526_1    bioconda
perl-test                 1.26                    pl526_1    bioconda
perl-test-deep            1.128                   pl526_1    bioconda
perl-test-differences     0.67                    pl526_0    bioconda
perl-test-exception       0.43                    pl526_2    bioconda
perl-test-harness         3.42                    pl526_0    bioconda
perl-test-leaktrace       0.16            pl526h14c3975_2    bioconda
perl-test-most            0.35                    pl526_0    bioconda
perl-test-requiresinternet 0.05                    pl526_0    bioconda
perl-test-warn            0.36                    pl526_1    bioconda
perl-text-balanced        2.03                    pl526_3    bioconda
perl-text-diff            1.45                    pl526_0    bioconda
perl-text-wrap            2013.0523               pl526_1    bioconda
perl-tie-ixhash           1.23                    pl526_2    bioconda
perl-time-hires           1.9760          pl526h14c3975_1    bioconda
perl-time-local           1.28                    pl526_1    bioconda
perl-timedate             2.30                    pl526_1    bioconda
perl-tree-dag_node        1.31                    pl526_0    bioconda
perl-try-tiny             0.30                    pl526_1    bioconda
perl-type-tiny            1.004004                pl526_0    bioconda
perl-types-serialiser     1.0                     pl526_2    bioconda
perl-unicode-map          0.112           pl526h6bb024c_3    bioconda
perl-uri                  1.76                    pl526_0    bioconda
perl-www-robotrules       6.02                    pl526_3    bioconda
perl-xml-dom              1.46                    pl526_0    bioconda
perl-xml-dom-xpath        0.14                    pl526_1    bioconda
perl-xml-filter-buffertext 1.01                    pl526_2    bioconda
perl-xml-libxml           2.0132          pl526h7ec2d77_1    bioconda
perl-xml-libxslt          1.94                    pl526_1    bioconda
perl-xml-namespacesupport 1.12                    pl526_0    bioconda
perl-xml-parser           2.44            pl526h4e0c4b3_7    bioconda
perl-xml-regexp           0.04                    pl526_2    bioconda
perl-xml-sax              1.02                    pl526_0    bioconda
perl-xml-sax-base         1.09                    pl526_0    bioconda
perl-xml-sax-expat        0.51                    pl526_3    bioconda
perl-xml-sax-writer       0.57                    pl526_0    bioconda
perl-xml-simple           2.25                    pl526_1    bioconda
perl-xml-twig             3.52                    pl526_2    bioconda
perl-xml-writer           0.625                   pl526_2    bioconda
perl-xml-xpath            1.44                    pl526_0    bioconda
perl-xml-xpathengine      0.14                    pl526_2    bioconda
perl-xsloader             0.24                    pl526_0    bioconda
perl-yaml                 1.29                    pl526_0    bioconda
pip                       20.0.2                     py_2    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
python                    3.7.6           h8356626_5_cpython    conda-forge
python_abi                3.7                     1_cp37m    conda-forge
r-base                    3.5.1             hc461eb7_1012    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
setuptools                46.1.3           py37hc8dfbb8_0    conda-forge
sqlite                    3.30.1               hcee41ef_0    conda-forge
t_coffee                  11.0.8           py37hea885bf_8    bioconda
tidyp                     1.04                          1    bioconda
tk                        8.6.10               hed695b0_0    conda-forge
tktable                   2.10                 h555a92e_3    conda-forge
wheel                     0.34.2                     py_1    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.9                h516909a_0    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxpm               3.5.13               h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-libxt                1.1.5             h516909a_1003    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.5                h516909a_0    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge
zstd                      1.4.4                h3b9ef0a_2    conda-forge

Juke34 commented 4 years ago

Thank you, I will see what I can do with that.

However, I can run the .pl scripts in /scratch/dro49/conda/envs/agat2/bin!

Calling them should not be a problem, but running one with data (agat_sp_gxf_to_gff3.pl with a gff input file) might be as at the beginning failing...

dakota-hawkins commented 4 years ago

Hey there,

Thanks for AGAT! I've been looking for an all-encompassing tool like this for a while, and AGAT seems to be exactly what I'm looking for.

I just want to pipe in that I've had the same issues described above. I've also been trying to install this on a shared cluster, and have a user-specific location where I'm trying to install to (again, no sudo access).

I am, however, able to install using conda install -c bioconda -c conda-forge agat on my local computer, and the program seems to work fine. Maybe this points to some build/install errors when lacking admin privileges?

The local working install was done on Elementary Linux while the cluster runs CentOS.

Rhinogradentia commented 4 years ago

Hi, I try to pack AGAT into a singularity container with the latest ubunut version to be able to run it on an HPC.

It was already necessary to manually copy the AGAT/Omniscient perl libraries manually into /etc/perlafter installing it with conda. Also the perl prerequisites weren't installed by conda and I had to install them manually using cpanm.

Inside the container I do have root privileges so this shouldn't be a problem.

When trying to run agat_convert_sp_gff2gtf.pl I got the following error:

singularity run agat.sif agat_convert_sp_gff2gtf.pl --gff Mpolymorphav3.1.allTrs.gff3 -o Mpolymorphav3.1.allTrs.gtf
converting to GTF3
********************************************************************************
*                              - Start parsing -                               *
********************************************************************************
-------------------------- parse options and metadata --------------------------
=> Accessing the feature level json files
Failed to find shared file 'features_level1.json' for dist 'AGAT' at /etc/perl/AGAT/OmniscientJson.pm line 128.

I've already tried to manually copy the json files but I think I got the wrong location - where exactly does agat expect those json files to be?

This is my installation. routine:

 cd /usr/local/miniconda/bin/ 
  ./conda update -y conda

  # configure conda channels
  ./conda config --add channels bioconda   
  apt install --no-install-recommends -y  r-base r-base-dev
   apt-get install -y cpanminus
   cpanm --with-recommends --quiet --force install IPC::Run
   cpanm --with-recommends --quiet --force Statistics::R
   cpanm --with-recommends --quiet install Clone Graph::Directed LWP::UserAgent JSON Carp Sort::Naturally
   cpanm --with-recommends --quiet --force install File::Share File::ShareDir::Install
   cpanm --with-recommends --quiet  --force install XML::DOM XML::DOM::XPath
   cpanm --with-recommends --quiet install Bio::Tools::GFF
   cpanm --with_recommends --quiet --force install Pod::Usage

  ./conda install -y -c bioconda agat
  ./conda update agat
   cp -r /usr/local/miniconda/lib/site_perl/5.26.2/AGAT /etc/perl/
   cp -r /usr/local/share/*.json /etc/perl/AGAT/
   cp -r /usr/local/share/*.obo /etc/perl/AGAT/

My version is 0.4.0

EDIT:

When installing it completely manually (old school) everything seems to work just fine.

Juke34 commented 4 years ago

Hi @Rhinogradentia, Singularity is able to use existing Docker images, and pull from Docker registries. We usually pull the AGAT image from quay.io when using it into Singularity. We do it in our nextflow pipelines. So I suggest you to follow this way instead if you want AGAT in a Singularity container.

Rhinogradentia commented 4 years ago

Hi @Rhinogradentia, Singularity is able to use existing Docker images, and pull from Docker registries. We usually pull the AGAT image from quay.io when using it into Singularity. We do it in our nextflow pipelines. So I suggest you to follow this way instead if you want AGAT in a Singularity container.

Hi @Juke34 , thanks a lot for the hint - I will give it a try. Best,

NBISweden / AGAT

AGAT cannot access features_level1.json file (wrong shared folder location detected by File::Share) #4