Hi,
Following the instructions on the ncbi website I installed Entrez Direct on my computer (MacOS). When I run the ncbi-provided script to confirm the installation in a new terminal everything is fine. But when I enter the bioinfo environment (after "conda activate bioinfo") I cannot confirm the installation:
$ cat installconfirm
***********************
esearch version:
11.0
xtract version:
EDirect install status:
***********************
(bioinfo)
and xtract gives the following error message:
$ xtract -version
-bash: /Users/myUserName/miniconda3/envs/bioinfo/bin/xtract: cannot execute binary file
(bioinfo)
If anyone knows a solution to this problem it would be of great help.
PS: echo $PATH has the ~/edirect folder
what are you trying with this command:
xtract -version | echo
?Should have been just: xtract -version Same issue
If you installed
entrezutils
in regular terminal (outside conda) then why are trying to run them from a conda environment?If you want to install inside your conda environment then do
once you activate that environment.
This didn't work for me and the issue is still the same
This is what I get:
Perhaps conda's macOS install for Entrezdirect is broken? In a fresh terminal (while not in a conda env) are you able to run
which esearch
andesearch -h
?I ran both commands in a fresh terminal (not in conda env)
"$ esearch -h" opened the help page
Precision: esearch works in the conda env, but not xtract