broken samtools in MacOS about binder

[amakunin]

Adding ncurses to environment.yml did not help and resulted in a bunch of inconsistencies:

The following packages are causing the inconsistency:

  - defaults/osx-64::jupyter_console==6.0.0=py36_0
  - defaults/osx-64::jupyterlab_server==0.2.0=py36_0
  - defaults/osx-64::widgetsnbextension==3.4.2=py36_0
  - pyviz/label/dev/noarch::holoviews==1.10.9=py_0
  - defaults/osx-64::nb_conda_kernels==2.2.0=py36_1
  - conda-forge/osx-64::bqplot==0.11.2=py36_1000
  - defaults/osx-64::ipython==7.2.0=py36h39e3cac_0
  - defaults/osx-64::jupyterlab==0.35.4=py36hf63ae98_0
  - defaults/osx-64::jupyter==1.0.0=py36_7
  - defaults/osx-64::ipywidgets==7.4.2=py36_0
  - defaults/osx-64::jupyterlab_launcher==0.13.1=py36_0
  - defaults/osx-64::qtconsole==4.4.3=py36_0
  - defaults/noarch::intake==0.4.4=py_0
  - defaults/osx-64::notebook==5.7.4=py36_0
  - defaults/osx-64::ipykernel==5.1.0=py36h39e3cac_0
  - intake/noarch::intake-xarray==0.2.4=py_0
failed

UPD: inconsistencies existed in the env prior to addition of ncurses

[amakunin]

Similar problem arose in the independent conda environment from EAGER which also includes samtools 1.9. This was installed on Sanger farm3. Error message:

  samtools: error while loading shared libraries: libtinfow.so.5: cannot open shared object file: No such file or directory

Googling also indicates the role of ncurses.

[amakunin]

Working MacOS test example:

Env:

name: samtoolstest
channels:
  - defaults
  - pyviz/label/dev
  - bokeh/label/dev
  - intake
  - bioconda
  - conda-forge
dependencies:
  - samtools=1.9
  - conda-forge::ncurses

Installed packages

# packages in environment at /Users/am60/malaria/malariagen/binder/conda/envs/samtoolstest:
#
# Name                    Version                   Build  Channel
bzip2                     1.0.6                h1de35cc_5  
ca-certificates           2019.5.15                     0  
curl                      7.64.1               ha441bb4_0  
krb5                      1.16.1               hddcf347_7  
libcurl                   7.64.1               h051b688_0  
libcxx                    4.0.1                hcfea43d_1  
libcxxabi                 4.0.1                hcfea43d_1  
libdeflate                1.0                  h1de35cc_1    bioconda
libedit                   3.1.20181209         hb402a30_0  
libssh2                   1.8.2                ha12b0ac_0  
ncurses                   6.1               h0a44026_1002    conda-forge
openssl                   1.1.1c               h1de35cc_1  
samtools                  1.9                 h7c4ea83_11    bioconda
tk                        8.6.8                ha441bb4_0  
xz                        5.2.4                h1de35cc_4  
zlib                      1.2.11               h1de35cc_3  

Adding - conda-forge::ncurses to binder environment also worked, so this should be a reasonable way to go forward (probably we need to fix the version, though). Previously I had some temporary issue during resolving dependencies.

[alimanfoo]

Happy to see a PR adding conda-forge::ncurses to requirements-conda.txt if that still works and would be useful.