Question: Unable to install samtools in macOS Catalina
0
gravatar for citronxu
8 weeks ago by
citronxu10
citronxu10 wrote:

Hi,there

I'm new in bioinformatics, and now working with macOS.

According to information given online, the new version of macOS - Catalina - due to the concern of security, the storage has been divided into two partitions, in which one named 'Macintosh HD' is read-only. When I tried to install samtools, found that operation was denies because of its read-only feature.

I'm wondering is there anyway to install samtools in macOS Catalina? by the way, I also tried use homebrew but failed as well. Or is it feasible to shift destination at which I'd like to install those softwares from the protected one into the other, which named 'Macintosh HD - data', and if it is, how?

many thanks in advance.

macos samtools • 181 views
ADD COMMENTlink modified 12 days ago by rank10 • written 8 weeks ago by citronxu10

In this case you have to compile (or install brew) on the partition that is writable.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by ATpoint36k

I set up Conda etc based on the Biostars manual. I did this in April. I have tried several ways to get samtools to work, and it does not work. I have seen that others have this problem, but I have not been able to track the route to a solution. Please help!

errors below:

Downloading and Extracting Packages
libcurl-7.71.1       | 305 KB    | ##################################### | 100% 
openssl-1.1.1g       | 1.9 MB    | ##################################### | 100% 
xz-5.2.5             | 227 KB    | ##################################### | 100% 
krb5-1.17.1          | 1.2 MB    | ##################################### | 100% 
curl-7.71.1          | 133 KB    | ##################################### | 100% 
libnghttp2-1.41.0    | 736 KB    | ##################################### | 100% 
samtools-1.4.1       | 494 KB    | ##################################### | 100% 
libev-4.33           | 100 KB    | ##################################### | 100% 
libssh2-1.9.0        | 212 KB    | ##################################### | 100% 
ncurses-6.2          | 902 KB    | ##################################### | 100% 
c-ares-1.16.1        | 92 KB     | ##################################### | 100% 
libedit-3.1.20191231 | 103 KB    | ##################################### | 100% 
libcxx-10.0.1        | 1.0 MB    | ##################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate samtools
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) 
nathanrank@Nathans-MacBook-Pro ~
$ conda activate samtools
(samtools) 
nathanrank@Nathans-MacBook-Pro ~
$ samtools
dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib
  Referenced from: /opt/miniconda3/envs/samtools/bin/samtools
  Reason: image not found
Abort trap: 6
(samtools)
ADD REPLYlink modified 12 days ago by Istvan Albert ♦♦ 84k • written 12 days ago by rank10

rerun the installation, not so long ago conda developed a problem where it pulls the wrong version of samtools,

the installation file has been recently updated to fix this error

# Activate the bioinformatics enviroment.
conda activate bioinfo

# Install most bioinformatics tools covered in the Biostar Handbook.
curl http://data.biostarhandbook.com/install/conda.txt | xargs conda install -y

if that does not work open an issue in the handbook tracker and we'll figure it out there

https://github.com/biostars/biostar-handbook-issues

ADD REPLYlink modified 12 days ago • written 12 days ago by Istvan Albert ♦♦ 84k

See this issue as well:

https://github.com/biostars/biostar-handbook-issues/issues/123

ADD REPLYlink written 12 days ago by Istvan Albert ♦♦ 84k
2
gravatar for genomax
8 weeks ago by
genomax87k
United States
genomax87k wrote:

Best way is possibly to use conda. Read more here. Once you have conda installed it is as simple as doing conda create -n samtools samtools followed by conda activate samtools.

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by genomax87k

many thanks for that, got samtools installed.:)

ADD REPLYlink written 8 weeks ago by citronxu10

nowadays this needs a version number otherwise it installs a wrong version and does not pull the proper libraries:

conda install samtools==1.10
ADD REPLYlink written 12 days ago by Istvan Albert ♦♦ 84k

Worked great for a while. Now I find myself having to reinstall it every time I want to use it.

ADD REPLYlink written 3 days ago by rank10
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