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flass / pantagruel

a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
GNU General Public License v3.0
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Task 5 failed: How to install lsd on server #32

Closed megaptera-helvetiae closed 4 years ago

megaptera-helvetiae commented 4 years ago

Hola Florent!

I tried to install lsd on our server but failed because I cannot use 'sudo'

It seems I need lsd. I would prefer doing all the steps of the pipeline on our server. Is there a way around it?

https://github.com/Peltoche/lsd

Here is my error:

/scratch/clamchatka/Panta/pantagruel/scripts/pipeline/pantagruel_pipeline_05_core_genome_ref_tree.sh: line 429: lsd: command not found
ERROR: failed ultrametrization of reference tree
ERROR: Pantagruel pipeline task 5: failed.
flass commented 4 years ago

Hi Laetitia,

yes you need LSD installed, but the software you mention above is not at all the one I mean (it is a fairly common acronym).

LSD, the one developed by O. Gascuel et al. for ultrametrisation of a phylogenetic tree, should already be installed through the execution of Pantagruel's install_dependencies.sh script.

If you want to install it manually, you can refer to the content of said script to see what needs to be done: (assuming that $SOFTWARE is where you mean to install you third-parrty software, and $BINS is a folder listed in your $PATH so that executables in there will be available in the command line).

cd ${SOFTWARE}/
wget https://github.com/tothuhien/lsd-0.3beta/releases/download/v0.3.3/lsd_unix
chmod +x ${SOFTWARE}/lsd_unix
ln -s ${SOFTWARE}/lsd_unix ${BINS}/lsd