I started getting in trouble with different programs installed using conda ('abricate', 'mlst') giving error messages with the Can't locate File/Slurp.pm in @INC. This occured after changing computers and having to reinstall different things and changing to anaconda3. As an example I get the following error message when trying to start abricate:
Can't locate File/Slurp.pm in @INC (you may need to install the File::Slurp module)
(@INC contains: /anaconda3/lib/perl5/site_perl/5.22.0/darwin-thread-multi-2level /anaconda3/lib/perl5/site_perl/5.22.0 /anaconda3/lib/perl5/5.22.0/darwin-thread-multi-2level /anaconda3/lib/perl5/5.22.0 .) at /anaconda3/bin/abricate line 9.
BEGIN failed--compilation aborted at /anaconda3/bin/abricate line 9.
when I search for the install on my computer it is already present in multiple locations (some of which are empty?):
I tried to reinstalling the slurp module
conda install -c bioconda perl-file-slurp
but that did not help.
I have tried to further understand how the @INC is build up. But I am confused about how this works with conda installed programs. When I look at the perl environment, I get different locations compared to the error message which specified different folders for the @INC.
$ env -i perl -V
Summary of my perl5 (revision 5 version 18 subversion 2) configuration:
Platform:
osname=darwin, osvers=18.0, archname=darwin-thread-multi-2level
uname='darwin osx337.sd.apple.com 18.0 darwin kernel version 17.0.0: fri may 4 10:33:38 pdt 2018; root:xnu-4570.1.46.100.2~1development_x86_64 x86_64 '
config_args='-ds -e -Dprefix=/usr -Dccflags=-g -pipe -Dldflags= -Dman3ext=3pm -Duseithreads -Duseshrplib -Dinc_version_list=none -Dcc=cc'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags =' -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -fstack-protector',
optimize='-Os',
cppflags='-g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -fstack-protector'
ccversion='', gccversion='4.2.1 Compatible Apple LLVM 10.0.0 (clang-1000.0.42)', gccosandvers=''
intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='cc', ldflags =' -fstack-protector'
libpth=/usr/lib /usr/local/lib
libs=
perllibs=
libc=, so=dylib, useshrplib=true, libperl=libperl.dylib
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=bundle, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags=' -bundle -undefined dynamic_lookup -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV PERL_SAWAMPERSAND USE_64_BIT_ALL
USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
USE_LOCALE USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_PERLIO USE_PERL_ATOF
USE_REENTRANT_API
Locally applied patches:
/Library/Perl/Updates/<version> comes before system perl directories
installprivlib and installarchlib points to the Updates directory
Built under darwin
Compiled at Aug 17 2018 17:29:08
@INC:
/Library/Perl/5.18/darwin-thread-multi-2level
/Library/Perl/5.18
/Network/Library/Perl/5.18/darwin-thread-multi-2level
/Network/Library/Perl/5.18
/Library/Perl/Updates/5.18.2
/System/Library/Perl/5.18/darwin-thread-multi-2level
/System/Library/Perl/5.18
/System/Library/Perl/Extras/5.18/darwin-thread-multi-2level
/System/Library/Perl/Extras/5.18
.
My path is as follows:
$ echo $PATH
/anaconda3/bin:/anaconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/ncbi/blast/bin:/opt/X11/bin
I believe it is also possible to change the environment by adding things to the program itself
use lib '/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level';
but as I have the problem with multiple programs I would like to understand what the core problem is (except me being rather new to this...:)
It looks like you have messed up your system.
If I interpret the messages correctly you have at least three different Perl installations:
osvers=18.0) installationenv -i CMD starts CMD with an empty environment, so it will remove anything you might have configured. So env -i perl -V will find the "default" perl in your system, which is the one from the macOS Mojave installation in /usr/bin/perl.
But that perl doesn't cause the error message, so we can ignore it.
When you execute conda ... it seems to use a perl 5.22.0 from /anaconda3. But at the same time you have installed perl 5.26.2 in that environment. My educated guess would be:
conda install runs (your question indicates that you want to use the "bioconda" channel?)So the first thing you should try is in the same terminal you ran conda in:
$ which perl
$ perl -V
How to fix this? Here are things I would try:
conda update -c bioconda perlconda remove -c bioconda perl and conda install -c bioconda perlrm -rf /anaconda3, removing the PATH additions from ~/.bashrc and then closing the terminal.