Question: Xtract (Entrez Direct) issue when in bioinfo environment
0
gravatar for benoit.duc
5 weeks ago by
benoit.duc0
benoit.duc0 wrote:

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

ADD COMMENTlink modified 23 days ago by Istvan Albert ♦♦ 82k • written 5 weeks ago by benoit.duc0

what are you trying with this command: xtract -version | echo?

ADD REPLYlink written 5 weeks ago by cpad011212k

Should have been just: xtract -version Same issue

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by benoit.duc0

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

conda install -c bioconda entrez-direct

once you activate that environment.

ADD REPLYlink written 5 weeks ago by genomax78k

This didn't work for me and the issue is still the same

ADD REPLYlink written 5 weeks ago by benoit.duc0

This is what I get:

$ conda install -c bioconda entrez-direct
Collecting package metadata (current_repodata.json): done
Solving environment: done
# All requested packages already installed.
ADD REPLYlink written 5 weeks ago by benoit.duc0

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 and esearch -h?

ADD REPLYlink written 5 weeks ago by genomax78k

I ran both commands in a fresh terminal (not in conda env)

$ which esearch
/Users/myUserName/edirect/esearch
(base)

"$ esearch -h" opened the help page

Precision: esearch works in the conda env, but not xtract

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by benoit.duc0
0
gravatar for Istvan Albert
23 days ago by
Istvan Albert ♦♦ 82k
University Park, USA
Istvan Albert ♦♦ 82k wrote:

The xtract command was rewritten in GO and it looks like the conda installation packages the wrong version of it but only in build pl526_1.

I have opened an issue with conda:

https://github.com/bioconda/bioconda-recipes/issues/20083

The binary versions for xtract are listed here:

Here is a quick and dirty fix on a Mac:

URL=https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/xtract.Darwin
curl $URL > `which xtract`

this will rewrite your copy of xtract with the proper binary version

ADD COMMENTlink modified 23 days ago • written 23 days ago by Istvan Albert ♦♦ 82k
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