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stajichlab / FGMP

Fungal Genome Mapping Pipeline
MIT License
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Installation issues with perl modules #18

Closed ZarulHanifah closed 4 years ago

ZarulHanifah commented 4 years ago

Following exactly the installation section, I came across this

$ ./FGMP/src/fgmp.pl
Can't locate IO/All.pm in @INC (you may need to install the IO::All module) (@INC contains: /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/site_perl/5.26.2 /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/5.26.2/x86_64-linux-thread-multi /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/5.26.2 .) at ./FGMP/src/fgmp.pl line 35.
BEGIN failed--compilation aborted at ./FGMP/src/fgmp.pl line 35.

Then I installed IO::All module

cpan -i IO::All

then I reran FGMP

$ ./FGMP/src/fgmp.pl
Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /home/ahbui/Zarul/BIN3890/FGMP/src/lib /home/ahbui/Zarul/BIN3890/FGMP/src/../lib /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/site_perl/5.26.2 /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/5.26.2/x86_64-linux-thread-multi /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/5.26.2 .) at /home/ahbui/Zarul/BIN3890/FGMP/src/../lib/FGMP.pm line 4.
BEGIN failed--compilation aborted at /home/ahbui/Zarul/BIN3890/FGMP/src/../lib/FGMP.pm line 4.
Compilation failed in require at ./FGMP/src/fgmp.pl line 41.
BEGIN failed--compilation aborted at ./FGMP/src/fgmp.pl line 41.

I thought I've already installed perl-bioperl? It still can't find where it is?

Feeling frustrated, I just attempted FGMP installation through conda

conda install -c bioconda -c conda-forge fgmp

Then I ran FGMP

$ fgmp
Can't locate FGMP.pm in @INC (you may need to install the FGMP module) (@INC contains: /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/bin/lib /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/bin/../lib/5.26.2/x86_64-linux-thread-multi /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/bin/../lib/5.26.2 /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/bin/../lib /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/site_perl/5.26.2 /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/5.26.2/x86_64-linux-thread-multi /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/5.26.2 .) at /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/bin/fgmp line 41.
BEGIN failed--compilation aborted at /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/bin/fgmp line 41.

I went to the closed issues, and thought that it had been resolved (https://github.com/stajichlab/FGMP/issues/12)?

Anyways, here is the list of software installed in the conda environment.

# packages in environment at /home/ahbui/Zarul/Software/anaconda3/envs/fgmp:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
augustus                  3.3.3           pl526h0faeac2_5    bioconda
bamtools                  2.5.1                he513fc3_6    bioconda
biopython                 1.78             py38h1e0a361_0    conda-forge
blast                     2.5.0                hc0b0e79_3    bioconda
boost                     1.70.0           py38h9de70de_1    conda-forge
boost-cpp                 1.70.0               h7b93d67_3    conda-forge
bzip2                     1.0.8                h516909a_3    conda-forge
c-ares                    1.11.0               h470a237_1    bioconda
ca-certificates           2020.6.20            hecda079_0    conda-forge
cdbtools                  0.99                 he513fc3_5    bioconda
certifi                   2020.6.20        py38h32f6830_0    conda-forge
diamond                   2.0.4                h56fc30b_0    bioconda
emboss                    6.6.0                h847b9ba_3    bioconda
exonerate                 2.4.0                haf93ef1_3    bioconda
expat                     2.2.9                he1b5a44_2    conda-forge
fgmp                      1.0.3                   pl526_1    bioconda
fontconfig                2.13.1            h1056068_1002    conda-forge
freetype                  2.10.2               he06d7ca_0    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
giflib                    5.2.1                h516909a_2    conda-forge
glib                      2.66.1               h680cd38_0    conda-forge
gsl                       2.6                  h294904e_0    conda-forge
hmmer                     3.3.1                he1b5a44_0    bioconda
htslib                    1.10.2               hd3b49d5_1    bioconda
icu                       67.1                 he1b5a44_0    conda-forge
jpeg                      9d                   h516909a_0    conda-forge
krb5                      1.17.1               hfafb76e_3    conda-forge
ld_impl_linux-64          2.35                 h769bd43_9    conda-forge
libblas                   3.8.0               17_openblas    conda-forge
libcblas                  3.8.0               17_openblas    conda-forge
libcurl                   7.71.1               hcdd3856_8    conda-forge
libdeflate                1.6                  h516909a_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 9.3.0               h5dbcf3e_17    conda-forge
libgd                     2.2.5             h341251c_1008    conda-forge
libgfortran-ng            7.5.0               hae1eefd_17    conda-forge
libgfortran4              7.5.0               hae1eefd_17    conda-forge
libgomp                   9.3.0               h5dbcf3e_17    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.8.0               17_openblas    conda-forge
libnghttp2                1.41.0               hab1572f_1    conda-forge
libopenblas               0.3.10          pthreads_hb3c22a3_4    conda-forge
libpng                    1.6.37               hed695b0_2    conda-forge
libssh2                   1.9.0                hab1572f_5    conda-forge
libstdcxx-ng              9.3.0               h2ae2ef3_17    conda-forge
libtiff                   4.1.0                hc7e4089_6    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp                   1.1.0                h56121f0_4    conda-forge
libwebp-base              1.1.0                h516909a_3    conda-forge
libxml2                   2.9.10               h68273f3_2    conda-forge
lp_solve                  5.5.2.5           h14c3975_1001    conda-forge
lz4-c                     1.9.2                he1b5a44_3    conda-forge
metis                     5.1.0             he1b5a44_1006    conda-forge
mysql-connector-c         6.1.11            h876a3cc_1006    conda-forge
ncurses                   6.2                  he1b5a44_1    conda-forge
numpy                     1.19.1           py38hbc27379_2    conda-forge
openssl                   1.1.1h               h516909a_0    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
perl                      5.26.2            h516909a_1006    conda-forge
perl-apache-test          1.40                    pl526_1    bioconda
perl-app-cpanminus        1.7044                  pl526_1    bioconda
perl-base                 2.23                    pl526_1    bioconda
perl-bioperl              1.6.924                       4    bioconda
perl-carp                 1.38                    pl526_3    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-constant             1.33                    pl526_1    bioconda
perl-cpan-meta            2.150010                pl526_0    bioconda
perl-cpan-meta-requirements 2.140                   pl526_0    bioconda
perl-cpan-meta-yaml       0.018                   pl526_0    bioconda
perl-data-dumper          2.173                   pl526_0    bioconda
perl-data-optlist         0.110                   pl526_2    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-dist-checkconflicts  0.11                    pl526_2    bioconda
perl-encode               2.88                    pl526_1    bioconda
perl-eval-closure         0.14            pl526h6bb024c_4    bioconda
perl-exporter             5.72                    pl526_1    bioconda
perl-extutils-cbuilder    0.280230                pl526_1    bioconda
perl-extutils-makemaker   7.36                    pl526_1    bioconda
perl-extutils-manifest    1.72                    pl526_0    bioconda
perl-extutils-parsexs     3.35                    pl526_0    bioconda
perl-file-path            2.16                    pl526_0    bioconda
perl-file-temp            0.2304                  pl526_2    bioconda
perl-file-which           1.23                    pl526_0    bioconda
perl-getopt-long          2.50                    pl526_1    bioconda
perl-io-tty               1.12                    pl526_1    bioconda
perl-ipc-cmd              1.02                    pl526_0    bioconda
perl-ipc-run              20180523.0              pl526_0    bioconda
perl-json-pp              4.04                    pl526_0    bioconda
perl-locale-maketext-simple 0.21                    pl526_2    bioconda
perl-module-build         0.4224                  pl526_3    bioconda
perl-module-corelist      5.20190524              pl526_0    bioconda
perl-module-implementation 0.09                    pl526_2    bioconda
perl-module-load          0.32                    pl526_1    bioconda
perl-module-load-conditional 0.68                    pl526_2    bioconda
perl-module-metadata      1.000036                pl526_0    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-mro-compat           0.13                    pl526_0    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-parallel-forkmanager 2.02                    pl526_0    bioconda
perl-params-check         0.38                    pl526_1    bioconda
perl-params-util          1.07            pl526h6bb024c_4    bioconda
perl-parent               0.236                   pl526_1    bioconda
perl-pathtools            3.75            pl526h14c3975_1    bioconda
perl-perl-ostype          1.010                   pl526_1    bioconda
perl-role-tiny            2.000008                pl526_0    bioconda
perl-scalar-list-utils    1.52            pl526h516909a_0    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-text-abbrev          1.02                    pl526_0    bioconda
perl-text-parsewords      3.30                    pl526_0    bioconda
perl-threaded             5.26.0                        0    bioconda
perl-try-tiny             0.30                    pl526_1    bioconda
perl-version              0.9924                  pl526_0    bioconda
perl-xsloader             0.24                    pl526_0    bioconda
perl-yaml                 1.29                    pl526_0    bioconda
pip                       20.2.3                     py_0    conda-forge
python                    3.8.5           h1103e12_9_cpython    conda-forge
python_abi                3.8                      1_cp38    conda-forge
readline                  8.0                  he28a2e2_2    conda-forge
setuptools                49.6.0           py38h32f6830_1    conda-forge
sqlite                    3.33.0               h4cf870e_0    conda-forge
suitesparse               5.7.2                h717dc36_0    conda-forge
tbb                       2020.2               hc9558a2_0    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
ucsc-fatotwobit           377                  h446ed27_3    bioconda
ucsc-twobitinfo           377                  h446ed27_1    bioconda
wheel                     0.35.1             pyh9f0ad1d_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h516909a_1009    conda-forge
zstd                      1.4.5                h6597ccf_2    conda-forge

Please help me. Thank you.

ocisse commented 4 years ago

Hi ZarulHanifah, Sorry for late reply and frustration. See my recommendation below

$ ./FGMP/src/fgmp.pl
Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /home/ahbui/Zarul/BIN3890/FGMP/src/lib /home/ahbui/Zarul/BIN3890/FGMP/src/../lib /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/site_perl/5.26.2 /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/5.26.2/x86_64-linux-thread-multi /home/ahbui/Zarul/Software/anaconda3/envs/fgmp/lib/5.26.2 .) at /home/ahbui/Zarul/BIN3890/FGMP/src/../lib/FGMP.pm line 4.
BEGIN failed--compilation aborted at /home/ahbui/Zarul/BIN3890/FGMP/src/../lib/FGMP.pm line 4.
Compilation failed in require at ./FGMP/src/fgmp.pl line 41.
BEGIN failed--compilation aborted at ./FGMP/src/fgmp.pl line 41.

perhaps just install bioperl (cpan will do)

conda install -c bioconda perl-bioperl

and make sure perl knows where fgmp lib is

export PERL5LIB="\$PERL5LIB:\$FGMP/lib"

FGMP conda installation often has platform specific issues. Try a fresh conda env first and if the problem persists let me know and I'll dig more 

conda install -c bioconda -c conda-forge fgmp

Thanks for using fgmp

ZarulHanifah commented 4 years ago

Thank you so much Ousmanne. It works on my computer now.

$ perl FGMP/src/fgmp.pl 

            fgmp

SOFTWARE:

        fgmp - 1.0.2

USAGE

    fgmp [options] -g < genome_fasta_file >

DESCRIPTION

REQUIRES
    fgmp requieres the installations of the following softwares

    - hmmer (HMMER 3.0) 
    - NCBI blast+
    - Exonerate
    - BioPerl xxx
    - IO::All
    - Emboss sixpack & csplit

ENVIRONMENT VARIABLES
    You can specific the path where the fgmp can find the default files
    with the shell variable "fgmp".

    o Using a Bourne-SHell
        export FGMP="path"
        export FGMPTMP="path"
        export PERL5LIB="$PERL5LIB:$FGMP/lib" 

COMMAND-LINE OPTIONS

        Available options and a short description are listed here; 

    -g, --genome        genome in fasta format

    -p, --protein       protein seeds

    -o, --output        output file prefix

    -d, --blastdb       blast database for the genome sequence

    -c, --cutoff_file   profiles cutoff file

    -m, --mark_file     completeness markers

    -r, --reads     reads

    --fuces_hmm     fungal Ultra Conserved Elements (hmms)

    --fuces_prefix       fungal Ultra Conserved Elements (names - one per line please!)

    --multicopies       default: multicopy genes from 1FKG data

    -t, --tag       tag to use OMA for fgmp, FUNY (Funybase) or CEG (cegma)

    -T, --threads       Specify the number of processor threads to use

    -v, --verbose       show progress

    -q, quiet       suppress show log

    -h, --help      show this help

    --tmp           keep temporary files

    -augTraingCutoff    specify the num of genes for augustus training

    --nsampleSize       Specify the # of samples for "SEARCH IN READS" module

    --nsampleSize       Specify the sample size for the "SEARCH IN READS" module

BUGS:
    Please report bugs to 'ousmanecis@gmail.com'.

AUTHORS:

    fgmp has been developped by Ousmane H. Cisse and Jason E. Stajich.

GNU-GPL (C)         date                 fgmp

Salam.

ocisse commented 4 years ago

Very happy to hear it. Thanks for the feedback.

Ousmane