Missing Apple Silicon (ARM) support in install.sh about biostar-handbook HOT 7 CLOSED

Hello,

I don't that this a correct fix, none of the bioinformatics tools run natively on ARM processors.

All tools run through the otherwise invisible Rosetta layer.

The problem occurs if the terminal is running in Rosetta, but entrez-direct was installed in native mode or vice-versa.

It is a problem of only entrez-direct specifically because it is the only tool that swaps out the executable at runtime based on architecture, regardless of how it was installed - had they run the original xtract command that was detected during the original install - either the M1 or the x64 one, it would run just fine.

It is a design flaw of entrez-direct. The problem is exactly that they are trying to guess the architecture.

The solution that I came up with is that we do not install entrez-direct into the conda environment anymore, but outside of it. And we don't recommend creating rosetta-based terminals either; there is no need for that.

There can still be issues if you have an older installation where we did install entrez-direct into conda.

The solution is to remove entrez-direct from conda and install it directly as:

yes | sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" > /dev/null

this is what the latest installers do.

from biostar-handbook.

Totally undestand.

Still there is a problem in the installation pipeline.

After cleaning and uninstalling everything, I proceeded thorugh a new installation and notice that I'm ending up with two entrez-direct installation.

Running which efetch with the base conda env or with conda totally disabled I get ~/miniconda3/envs/bioinfo/bin/efetch. Running the same command inside bioinfo env I get ~/edirect/efetch.

So I installed conda-tree, that provides a tool to see the dependency tree in conda, and running the command conda-tree whoneeds entrez-direct returns blast.

In install.sh when the command curl -s http://data.biostarhandbook.com/install/conda.txt | xargs mamba install -q -y is run and blast instaled, also entrez-direct is installed.

This generates the problem reported here https://www.biostars.org/p/9559937/ for all Mac ARM users

from biostar-handbook.

One possible solution would be to check if the platform is Darwin arm64 and add the following lines:

cd ~/miniconda3/envs/bioinfo/bin/

nquire -dwn ftp.ncbi.nlm.nih.gov entrez/entrezdirect rchive.Silicon.gz
nquire -dwn ftp.ncbi.nlm.nih.gov entrez/entrezdirect transmute.Silicon.gz
nquire -dwn ftp.ncbi.nlm.nih.gov entrez/entrezdirect xtract.Silicon.gz

gunzip -f *.gz

chmod +x rchive.Silicon
chmod +x transmute.Silicon
chmod +x xtract.Silicon

And maybe no installation outside bioinfo would be needed?

from biostar-handbook.

Ok, an interesting and annoying problem with entrez-direct, thanks for tracking down that dependency issue; that helps immensely. I have been scratching my head of how you ended up with two versions.

The crux of the problem is that manually installed entrez-direct alters the PATH so that its directory comes after bioconda search PATH.

PATH=$PATH/~/edirect

Thus we end up triggering the wrong version of it.

so I think a simpler solution is not to allow the manual install to alter the path, then the have the install.sh add

PATH=~/edirect;$PATH

from biostar-handbook.

Since there's no control over the entrez installation script what about adding the following lines after step 9:

mv ~/.bashrc ~/.bashrc.bk

# Prints all the lines expect the last one
awk 'NR>1{print prev} {prev=$0}' ~/.bashrc.bk > ~/.bashrc

echo 'export PATH=~/edirect:${PATH}' >> ~/.bashrc

rm -f ~/.bashrc.bk 

Otherwise, if you don't want to delete from .bashrc:

echo 'export PATH=~/edirect:$(echo $PATH | rev | cut -d ':' -f 2- | rev)'  >> ~/.bashrc

Both soultions work for me.

from biostar-handbook.

I think there is control over the process PATH extension process as it asks for permission to append to .bashrc, so I think, amusingly the solution would be to install with yes no:

yes no | sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" > /dev/null

Then the .biostar.sh that is sourced from .bashrc will contain the PATH extension and will be applied right away.

I have made both changes now and will test it out soon, right now there are problems with NCBI, it seems, something is very slow on their site

from biostar-handbook.

Marking this issue as completed since the fix works

from biostar-handbook.