dat-ecosystem-archive / anacapa-container Goto Github PK

I just wanted to document some issues i ran into when following the installation instructions (on my personal macbook)

1. make sure to run everything as root

after you open the shell, type sudo -i and enter your password

see https://stackoverflow.com/a/31711279/1183277

2. If you follow the instruction to install vagrant https://singularity.lbl.gov/install-mac

note that

brew cask install virtualbox
brew cask install vagrant
brew cask install vagrant-manager

must now be typed as

brew install --cask virtualbox
brew install --cask vagrant
brew install --cask vagrant-manager

see https://stackoverflow.com/a/66081492

3. when you run vagrant init singularityware/singularity-2.4 it will fail

You need to go to Sytem preferences > Security & Privacy. Some Oracle thing will be there and you need to allow it and restart

(However, I think just must let it fail for the option to appear, but not sure)

see hashicorp/vagrant#12049 (comment)

After I troubleshooted these steps above, I managed to install vagrant. However see also #6 (correct path to image)

Hi @joehand could you give @limey-bean and @zjgold push access here? They might wanna do readme updates etc in the future.

hey Max, great container. trying to get this up and running on our new server in the Barber lab. We were a little stumped by the copy url instructions to download from zenodo. We ended up copying the link of each of three datasets. Is there a url to download all three at once? Was not clear. Thanks

Hello,

I am trying to run this container in Hoffman2. I've downloaded all the files and the singularity seems to be working fine. The issue is when I try to run the first script, the Anacapa QC step. I've followed the instructions and edited the paths. But when I run the script using sh run-anacapa-qc.sh, I get the following warning and no output:

INFO:    Converting SIF file to temporary sandbox...
/u/local/Modules/4.7.0/gcc-4.8.5/init/bash: line 37: /usr/bin/tclsh: No such file or directory
/u/local/Modules/4.7.0/gcc-4.8.5/init/bash: line 37: /usr/bin/tclsh: No such file or directory

Running in HPC mode
No username given...

INFO:    Cleaning up image...

real    0m16.936s
user    0m14.808s
sys     0m13.375s

I've edited the script to have my Hoffman2 username:

time singularity exec --userns -B $BASEDIR $CONTAINER /bin/bash -c $DB/anacapa_QC_dada2.sh -i $DATA -o $OUT -u rturba -d $DB -f $FORWARD -r $REVERSE -e $DB/metabarcode_loci_min_merge_length.txt -a truseq -t MiSeq -g

But I still get the same warning. I don't know what is happening.

I have followed the instructions to install the Vagrant virtual machine on mac osx (Big Sour)

it seems to work. From within vagrant I get this:

vagrant@vagrant:~$ ls /vagrant
Vagrantfile  anacapa-1.5.0.img  anacapa_db_vagrant

However, loading the image fails

vagrant@vagrant:~$ singularity shell  /usr/local/singularity-vm/anacapa-1.5.0.img 
ERROR  : Image path doesn't exists
ABORT  : Retval = 255

I noted that the instruction say

This guide was tested with Singularity version 2.5.2.

However, when installing Singularity in the virtual box following the instructions here https://singularity.lbl.gov/install-mac

Install singularity 2.4 and no more recent version seems to be available.

vagrant@vagrant:~$ singularity --version
2.4-dist

Would you have any pointers?