Run bash script in Perl program !
...fferent functions. Despite the fact that Python is commonly favoured over Perl, some bioinformatics software, such as the standalone version of 'alienomics', is written in Perl. Often i...668 days ago
Read a tab delimited file and search with perl
use strict; use warnings; use Data::Dumper; use Text::CSV; use IO::Handle; my $file = "/home/urbe/Tools/Alienomics_v0.1/Alienomics/output/intermediate_files/rRNA/refGene.megablast"; open my $fh, "[0]\n"; warn Dumper $row; # To see the structure }2556 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...rint "\n Module $_ OK!\n";} } # end 'for' } # end 'BEGIN' block #Bash script else here print "\nDownloading third party database for Alienomics\n"; #Install NCBI taxdump...1191 days ago
Alienomics "environment is inconsistent" error ?
$ conda install -c jnarayan81 alienomics The environment is inconsistent, please check the package plan carefullyThe following packages are causing the inconsistency: - defaults/linux-64::jupyter==1.0.0=py37_7 - defaults/noarch::pygments==2.5.2=py_0 - defaults/noarch::jupyter_c...Tags: Alienomics, error, inconsistent, conda, package, install
1205 days ago
GLIBC_2.23' not found error with alienomics !
(base) lege@Bathymodiolus:~$ ./alienomics_v0.3.1Can't load '/tmp/par-6a6974656e647261/cache-f3e57c2becbb7e00629c1273cf03dd05ad45721b/5b8c5ac2.so' for module POSIX: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/par-6a6974656e647261/cache-f3e57c2becbb7e00629c1273...Tags: alienomics, error, GLIBC_2.23, not, found, bug, OS
1170 days ago