How to install with conda/mamba ?

[Fred-07]

Hi, Installation from the environmeent file does not work:

mamba  env create -f ChameleolyserEnvironment.yml
bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
pkgs/r/noarch                                                 No change
pkgs/main/linux-64                                            No change
pkgs/main/noarch                                              No change
pkgs/r/linux-64                                               No change

Looking for: ['_libgcc_mutex==0.1=conda_forge', '_openmp_mutex==4.5=1_gnu', '_r-mutex==1.0.1=anacondar_1', 'bbmap==38.56=h14c3975_0', 'bedops==2.4.36=h6bb024c_1', 'bedtools==2.28.0=hdf88d34_0', 'bwa==0.7.17=h7132678_9', 'bzip2==1.0.8=h7f98852_4', 'ca-certificates==2021.10.8=ha878542_0', 'cairo==1.16.0=h9f066cc_1006', 'curl==7.71.1=he644dc0_3', 'expat==2.4.8=h27087fc_0', 'font-ttf-dejavu-sans-mono==2.37=hab24e00_0', 'font-ttf-inconsolata==3.000=h77eed37_0', 'font-ttf-source-code-pro==2.038=h77eed37_0', 'font-ttf-ubuntu==0.83=hab24e00_0', 'fontconfig==2.14.0=h8e229c2_0', 'fonts-conda-ecosystem==1=0', 'fonts-conda-forge==1=0', 'freetype==2.10.4=h0708190_1', 'fribidi==1.0.10=h36c2ea0_0', 'gatk4==4.1.2.0=1', 'gettext==0.19.8.1=hf34092f_1004', 'graphite2==1.3.13=h58526e2_1001', 'harfbuzz==2.7.2=ha5b49bf_1', 'htslib==1.9=ha228f0b_7', 'icu==67.1=he1b5a44_0', 'jpeg==9e=h7f98852_0', 'krb5==1.17.2=h926e7f8_0', 'libcurl==7.71.1=hcdd3856_3', 'libdeflate==1.0=h14c3975_1', 'libedit==3.1.20191231=h46ee950_2', 'libffi==3.2.1=he1b5a44_1007', 'libgcc==7.2.0=h69d50b8_2', 'libgcc-ng==11.2.0=h1d223b6_14', 'libglib==2.66.3=hbe7bbb4_0', 'libgomp==11.2.0=h1d223b6_14', 'libiconv==1.16=h516909a_0', 'libpng==1.6.37=h21135ba_2', 'libssh2==1.10.0=ha56f1ee_2', 'libstdcxx-ng==11.2.0=he4da1e4_14', 'libtiff==4.0.10=hc3755c2_1005', 'libuuid==2.32.1=h7f98852_1000', 'libxcb==1.13=h7f98852_1004', 'libxml2==2.9.10=h68273f3_2', 'libzlib==1.2.11=h166bdaf_1014', 'lofreq==2.1.3.1=py36_0', 'lz4-c==1.9.3=h9c3ff4c_1', 'ncurses==6.1=hf484d3e_1002', 'openjdk==8.0.312=h7f98852_0', 'openssl==1.1.1n=h166bdaf_0', 'pango==1.42.4=h69149e4_5', 'pcre==8.45=h9c3ff4c_0', 'perl==5.26.2=h36c2ea0_1008', 'perl-carp==1.38=pl526_3', 'perl-config-general==2.63=pl526_0', 'perl-exporter==5.72=pl526_1', 'perl-extutils-makemaker==7.36=pl526_1', 'perl-pathtools==3.75=pl526h14c3975_1', 'picard==2.20.8=0', 'pip==21.3.1=pyhd8ed1ab_0', 'pixman==0.40.0=h36c2ea0_0', 'pthread-stubs==0.4=h36c2ea0_1001', 'python==3.6.7=h381d211_1004', 'python_abi==3.6=2_cp36m', 'r-base==3.2.2=0', 'readline==7.0=hf8c457e_1001', 'samtools==1.9=h10a08f8_12', 'setuptools==58.0.4=py36h5fab9bb_2', 'sqlite==3.28.0=h8b20d00_0', 'tk==8.6.12=h27826a3_0', 'wheel==0.37.1=pyhd8ed1ab_0', 'xorg-kbproto==1.0.7=h7f98852_1002', 'xorg-libice==1.0.10=h7f98852_0', 'xorg-libsm==1.2.3=hd9c2040_1000', 'xorg-libx11==1.7.2=h7f98852_0', 'xorg-libxau==1.0.9=h7f98852_0', 'xorg-libxdmcp==1.1.3=h7f98852_0', 'xorg-libxext==1.3.4=h7f98852_1', 'xorg-libxrender==0.9.10=h7f98852_1003', 'xorg-renderproto==0.11.1=h7f98852_1002', 'xorg-xextproto==7.3.0=h7f98852_1002', 'xorg-xproto==7.0.31=h7f98852_1007', 'xz==5.2.5=h516909a_1', 'zlib==1.2.11=h166bdaf_1014', 'zstd==1.4.9=ha95c52a_0']

Encountered problems while solving:
  - nothing provides requested r-base ==3.2.2 0
  - nothing provides icu 54.* needed by r-base-3.3.1-1

[WouterSteyaert]

Hi,

A couple of questions:

What is the operating system that you use? Could you try installing icu separatly? Do you have r installed in your environment?

Best wishes Wouter

[Fred-07]

Hi Wouter,

I tried on CentOS6 cluster and on Ubuntu 20 machine. Following your message, I tried on a fresh Ubuntu installation (VirtualBox) and the message is : conda env create -f ChameleolyserEnvironment.yml Collecting package metadata (repodata.json): done Solving environment: failed

ResolvePackageNotFound:

• r-base==3.2.2=0

It seems that ChameleolyserEnvironment.yml cannot be used. Or is it necessary to install other dependencies before ?

Thanks Best wishes

[WouterSteyaert]

Hi Fred,

You are right, I replicated your error. Now it should work however. Let me know if you experience any issues.

Best wishes, Wouter