Я использую conda для установки нескольких пакетов. Я уже установил Perl под conda, и он работает на этой машине (работает под управлением Ubuntu 18.04). Сейчас я пытаюсь использовать скрипт, который требует bioperl.
Я попытался обновить conda, установить bioperl через conda И установить bioperl через cpanm, как показано ниже.
Я проверил, используется ли Perl в настоящее время как анаконда. Шебанг в сценарии perl: #!/home/evo-slave/anaconda_ete/bin/perl -w
Это первоначальная ошибка при запуске сценария
Can't locate Bio/SeqIO.pm in @INC (you may need to install the
Bio::SeqIO module) (@INC contains: /home/evo-
slave/anaconda_ete/lib/site_perl/5.26.2/x86_64-linux-thread-multi
/home/evo-slave/anaconda_ete/lib/site_perl/5.26.2 /home/evo-
slave/anaconda_ete/lib/5.26.2/x86_64-linux-thread-multi /home/evo-
slave/anaconda_ete/lib/5.26.2 .) at ./cortador.pl line 9.
BEGIN failed--compilation aborted at ./cortador.pl line 9.
Я не знаю, является ли проблема в том, что bioperl не вызывается /установленный perl anaconda или во время выполнения сценария, возможно, эти строки в сценарии должны указывать на что-то еще
use File::Basename;
use Bio::SeqIO;
use Bio::Seq;
use Bio::DB::SeqFeature::Store;
use Bio::SeqFeatureI;
Когда я пытаюсь установить
cpanm Bio::Perl
Я получил эту ошибку
--> Working on Bio::Perl
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-
1.007002.tar.gz ... OK
Configuring BioPerl-1.007002 ... OK
==> Found dependencies: IO::String, Data::Stag, Test::Most
--> Working on IO::String
Fetching http://www.cpan.org/authors/id/G/GA/GAAS/IO-String-
1.08.tar.gz ... OK
Configuring IO-String-1.08 ... OK
Building and testing IO-String-1.08 ... OK
Successfully installed IO-String-1.08
--> Working on Data::Stag
Fetching http://www.cpan.org/authors/id/C/CM/CMUNGALL/Data-Stag-
0.14.tar.gz ... OK
Configuring Data-Stag-0.14 ... OK
==> Found dependencies: IO::String
! Installing the dependencies failed: Module 'IO::String' is not
installed
! Bailing out the installation for Data-Stag-0.14.
--> Working on Test::Most
Fetching http://www.cpan.org/authors/id/O/OV/OVID/Test-Most-
0.35.tar.gz ... OK
Configuring Test-Most-0.35 ... OK
==> Found dependencies: Test::Warn, Test::Deep, Test::Differences,
Test::Exception, Exception::Class
--> Working on Test::Warn
Fetching http://www.cpan.org/authors/id/B/BI/BIGJ/Test-Warn-
0.36.tar.gz ... OK
Configuring Test-Warn-0.36 ... OK
==> Found dependencies: Sub::Uplevel
--> Working on Sub::Uplevel
Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/Sub-Uplevel-
0.2800.tar.gz ... OK
Configuring Sub-Uplevel-0.2800 ... OK
Building and testing Sub-Uplevel-0.2800 ... OK
Successfully installed Sub-Uplevel-0.2800
! Installing the dependencies failed: Module 'Sub::Uplevel' is not
installed
! Bailing out the installation for Test-Warn-0.36.
--> Working on Test::Deep
Fetching http://www.cpan.org/authors/id/R/RJ/RJBS/Test-Deep-
1.128.tar.gz ... OK
Configuring Test-Deep-1.128 ... OK
Building and testing Test-Deep-1.128 ... OK
Successfully installed Test-Deep-1.128
--> Working on Test::Differences
Fetching http://www.cpan.org/authors/id/D/DC/DCANTRELL/Test-
Differences-0.67.tar.gz ... OK
Configuring Test-Differences-0.67 ... OK
==> Found dependencies: Capture::Tiny, Text::Diff
--> Working on Capture::Tiny
Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/Capture-
Tiny-0.48.tar.gz ... OK
Configuring Capture-Tiny-0.48 ... OK
Building and testing Capture-Tiny-0.48 ... OK
Successfully installed Capture-Tiny-0.48
--> Working on Text::Diff
Fetching http://www.cpan.org/authors/id/N/NE/NEILB/Text-Diff-
1.45.tar.gz ... OK
Configuring Text-Diff-1.45 ... OK
==> Found dependencies: Algorithm::Diff
--> Working on Algorithm::Diff
Fetching http://www.cpan.org/authors/id/T/TY/TYEMQ/Algorithm-Diff-
1.1903.tar.gz ... OK
Configuring Algorithm-Diff-1.1903 ... OK
Building and testing Algorithm-Diff-1.1903 ... OK
Successfully installed Algorithm-Diff-1.1903
! Installing the dependencies failed: Module 'Algorithm::Diff' is
not installed
! Bailing out the installation for Text-Diff-1.45.
! Installing the dependencies failed: Module 'Text::Diff' is not
installed, Module 'Capture::Tiny' is not installed
! Bailing out the installation for Test-Differences-0.67.
--> Working on Test::Exception
Fetching http://www.cpan.org/authors/id/E/EX/EXODIST/Test-
Exception-0.43.tar.gz ... OK
Configuring Test-Exception-0.43 ... OK
==> Found dependencies: Sub::Uplevel
! Installing the dependencies failed: Module 'Sub::Uplevel' is not
installed
! Bailing out the installation for Test-Exception-0.43.
--> Working on Exception::Class
Fetching http://www.cpan.org/authors/id/D/DR/DROLSKY/Exception-
Class-1.44.tar.gz ... OK
Configuring Exception-Class-1.44 ... OK
==> Found dependencies: Class::Data::Inheritable
--> Working on Class::Data::Inheritable
Fetching http://www.cpan.org/authors/id/T/TM/TMTM/Class-Data-
Inheritable-0.08.tar.gz ... OK
Configuring Class-Data-Inheritable-0.08 ... OK
Building and testing Class-Data-Inheritable-0.08 ... OK
Successfully installed Class-Data-Inheritable-0.08
! Installing the dependencies failed: Module
'Class::Data::Inheritable' is not installed
! Bailing out the installation for Exception-Class-1.44.
! Installing the dependencies failed: Module 'Test::Exception' is
not installed, Module 'Test::Differences' is not installed, Module
'Exception::Class' is not installed, Module 'Test::Warn' is not
installed, Module 'Test::Deep' is not installed
! Bailing out the installation for Test-Most-0.35.
! Installing the dependencies failed: Module 'Test::Most' is not
installed, Module 'IO::String' is not installed, Module
'Data::Stag'
is not installed
! Bailing out the installation for BioPerl-1.007002.
6 distributions installed
ETA : Кажется, что-то не так, и необходимые модули не устанавливаются во время простого cpanm. Пример раунда, пытающегося установить все, что нужно
cpanm Sub::Uplevel
--> Working on Sub::Uplevel
Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/Sub-Uplevel-0.2800.tar.gz ... OK
Configuring Sub-Uplevel-0.2800 ... OK
Building and testing Sub-Uplevel-0.2800 ... OK
Successfully installed Sub-Uplevel-0.2800
1 distribution installed
затем
cpanm Test::Warn
--> Working on Test::Warn
Fetching http://www.cpan.org/authors/id/B/BI/BIGJ/Test-Warn-0.36.tar.gz ... OK
Configuring Test-Warn-0.36 ... OK
==> Found dependencies: Sub::Uplevel
--> Working on Sub::Uplevel
Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/Sub-Uplevel-0.2800.tar.gz ... OK
Configuring Sub-Uplevel-0.2800 ... OK
Building and testing Sub-Uplevel-0.2800 ... OK
Successfully installed Sub-Uplevel-0.2800
! Installing the dependencies failed: Module 'Sub::Uplevel' is not installed
! Bailing out the installation for Test-Warn-0.36.
1 distribution installed
Некоторая информация, помогающая при отладке:
$ set | grep ^PERL
PERL5LIB=:/media/evo-slave/Disco2/ANDRES/DOWNLOADS/GENOME/CAV-POC/GAAS/annotation
PERL_MB_OPT='--install_base "/home/evo-slave/perl5"'
PERL_MM_OPT=INSTALL_BASE=/home/evo-slave/perl5
$ which cpanm
/home/evo-slave/anaconda_ete/bin/cpanm
$ head -n 1 "$( which cpanm )"
#!/home/evo-slave/anaconda_ete/bin/perl