Problem with installing viewBS

hyl317 commented 4 years ago

Hi, so I tried to install viewBS on Debian and got the following error. It seems like I am missing one package in my conda; so I checked the /anaconda3/pkgs , and turns out I have libuuid-1.0.3-h1bed415_2 and libssh2-1.8.0-h5b517e9_2 but not the exact version as shown in the error message. I tried to install these package, yet I couldn't find that particular version. Any help?

yh362@mocha:~/tools/ViewBS-0.1.8$ conda env create --name env_ViewBS --file environment.yaml
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound:
  - libssh2==1.8.0=h5b517e9_3
  - libuuid==1.0.3=1

xie186 commented 4 years ago

Could you please try the file attached here? environment.txt Please let me know if it works. Thanks.

conda env create --name env_ViewBS --file environment.txt

hyl317 commented 4 years ago

If I use the new environment.txt, I got

yh362@mocha:~/tools/ViewBS-0.1.8$ conda env create --name env_ViewBS --file environment.txt

CondaValueError: invalid package specification: name: env_ViewBS

xie186 commented 4 years ago

Please try this one environment.txt

hyl317 commented 4 years ago

emm.. I got the same error message.

xie186 commented 4 years ago

Could you please show your conda version?

conda -V

hyl317 commented 4 years ago

yh362@mocha:~$ conda --version conda 4.7.9

hyl317 commented 4 years ago

Replacing libssh2==1.8.0=h5b517e9_3 with libssh2==1.8.0 and libuuid==1.0.3=1 with libuuid==1.0.3 in the original environment.yaml file seems to solve the problem. Thx!

xie186 commented 4 years ago

Thanks. In the file provided here https://github.com/xie186/ViewBS/issues/37#issuecomment-513777556, I removed "build specification from dependencies" (eg. =h5b517e9_3). Instead of run:

wget https://github.com/xie186/ViewBS/files/3417395/environment.txt
conda env create --name env_ViewBS --file environment.txt

we should run:

wget https://github.com/xie186/ViewBS/files/3417395/environment.txt
mv environment.txt environment.yaml
conda env create --name env_ViewBS --file environment.yaml

The suffix of the environment file matters here. But .yaml file is not allowed to be attached. If possible, please help me have a try.

hyl317 commented 4 years ago

On my system, the environment is already there (CondaValueError: prefix already exists: /home/yh362/anaconda3/envs/env_ViewBS). But I can ask if someone else in my lab would like to have a try tomorrow. Thx for timely reply!

aer-neo commented 4 years ago

hello, I got the same error message.

conda env create --name env_ViewBS --file environment.yaml Collecting package metadata: done Solving environment: failed

ResolvePackageNotFound:

libuuid==1.0.3=1
libssh2==1.8.0=h5b517e9_3

I tried to run:

wget https://github.com/xie186/ViewBS/files/3417395/environment.txt mv environment.txt environment.yaml conda env create --name env_ViewBS --file environment.yaml

and, i got this:

conda env create --name env_ViewBS --file environment.yaml

Collecting package metadata: done Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:

libssh2=1.8.0
r-pillar=1.3.1 -> r-base[version='>=3.6,<3.7.0a0'] -> libcurl[version='>=7.64.1,<8.0a0'] -> libssh2[version='>=1.8.2,<1.9.0a0'] Use "conda search --info" to see the dependencies for each package.

xie186 commented 4 years ago

I'm not sure why conda give the error message above. I think it's the problem of conda. I'll try to collect more information to solve this problem. Currently I suggest you to either follow the instructions here (https://github.com/xie186/ViewBS#installation-of-dependencies-step-by-step) to install or generate the environment using the command lines below:

conda create -n env_ViewBS
conda activate env_ViewBS
conda install -c anaconda perl
conda install -c bioconda perl-bio-db-hts 
conda install -c bioconda perl-bioperl 
conda install -c bioconda perl-app-cpanminus 
cpanm Getopt::Long::Subcommand
conda install -c r r-ggplot2 
conda install -c bioconda r-pheatmap 
conda install -c r r-reshape2 
conda install -c conda-forge r-cowplot

Please let me know if you still have any other problems.

avellab commented 4 years ago

Hello, I tried above script you mentioned, it didnt give me any error but when I used conda info --envs , the environment is not created.

wget https://github.com/xie186/ViewBS/files/3417395/environment.txt mv environment.txt environment.yaml conda env create --name env_ViewBS --file environment.yaml

he-yunxiao commented 3 years ago

Hello, I tried to install viewBS on Debian and got the following error，can you give me some adivice？When i ./ViewBS,it tell me 'Can't locate Bio/DB/HTS/Tabix.pm in @INC (you may need to install the Bio::DB::HTS::Tabix module)'. then i install the Bio::DB::HTS::Tabix module,it tell me ' Configure failed for Bio-DB-HTS-3.01. See /home/data/vip05/.cpanm/work/1608864197.2299507/build.log for details.'

he-yunxiao commented 3 years ago

details: cpanm (App::cpanminus) 1.7044 on perl 5.026002 built for x86_64-linux-thread-multi Work directory is /home/data/vip05/.cpanm/work/1608862721.2139162 You have make /usr/bin/make You have LWP 6.39 You have /usr/bin/tar: tar (GNU tar) 1.30 Copyright (C) 2017 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later https://gnu.org/licenses/gpl.html. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason. You have /usr/bin/unzip Searching Bio::DB::HTS::Tabix () on cpanmetadb ... --> Working on Bio::DB::HTS::Tabix Fetching http://www.cpan.org/authors/id/A/AV/AVULLO/Bio-DB-HTS-3.01.tar.gz -> OK Unpacking Bio-DB-HTS-3.01.tar.gz Entering Bio-DB-HTS-3.01 Checking configure dependencies from META.json Checking if you have ExtUtils::Install 1.46 ... Yes (2.06) Checking if you have Module::Build 0.38 ... Yes (0.4231) Configuring Bio-DB-HTS-3.01 Running Build.PL Can't exec "/tmp/build/80754af9/perl_1527832170752/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc": No such file or directory at /home/data/vip05/anaconda3/envs/BS/lib/site_perl/5.26.2/ExtUtils/CBuilder/Base.pm line 342. Warning: ExtUtils::CBuilder not installed or no compiler detected Proceeding with configuration, but compilation may fail during Build

This module requires HTSlib (http://htslib.org/) Install it if you have not done so already.

This script will attempt to locate HTSlib by looking for htslib/hts.h and libhts.a / libhts.so in:

--htslib command line argument
HTSLIB_DIR environment variable
--prefix command line argument (which also sets installation location)
Alien::HTSlib dependency resolver
pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
common library locations: /usr /usr/local, /usr/share, /opt/local

-> N/A -> FAIL Configure failed for Bio-DB-HTS-3.01. See /home/data/vip05/.cpanm/work/1608862721.2139162/build.log for details.

he-yunxiao commented 3 years ago

But what makes me sad is i have already installed ExtUtils::CBuilde.

acontrerasg commented 3 years ago

I'm not sure why conda give the error message above. I think it's the problem of conda. I'll try to collect more information to solve this problem. Currently I suggest you to either follow the instructions here (https://github.com/xie186/ViewBS#installation-of-dependencies-step-by-step) to install or generate the environment using the command lines below:
conda create -n env_ViewBS
conda activate env_ViewBS
conda install -c anaconda perl
conda install -c bioconda perl-bio-db-hts 
conda install -c bioconda perl-bioperl 
conda install -c bioconda perl-app-cpanminus 
cpanm Getopt::Long::Subcommand
conda install -c r r-ggplot2 
conda install -c bioconda r-pheatmap 
conda install -c r r-reshape2 
conda install -c conda-forge r-cowplot 
Please let me know if you still have any other problems. Hello there, I just wanted to chime in and say that this is the only way I managed to installed on Linux 4.19.140 x86_64. Thanks!

xie186 / ViewBS

Problem with installing viewBS #37