can anyone give me a hand to install sm-assemblies?

[pomidorku]

Hi,

I am trying to install sm_assemblies in an ubuntu 18.04 machine.

I installed conda first of all.
The specifications of my conda installation are as follows:
conda 4.8.2
Python 3.6.7

Next, I created an environment for sm_assemblies and inside the environment I installed the following:

conda install -c bioconda -c conda-forge snakemake
conda install -c conda-forge biopython
conda install -c bioconda blat
conda install -c bioconda ncbitk (just in case)
conda install -c anaconda wget
conda install -c bioconda samtools

I did clone the https://github.com/WatsonLab/sm_assemblies.git into my home directory.

The list of dependencies I CANNOT install:

splign (https://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi?textpage=downloads)
I did wget ftp://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/splign/linux-i64/splign.tar.gz
but I cannot find a way to install it in conda. How to install it in conda? I am kind of newbie to linux.

Python 3.5 (I HAVE PYTHON 3.6.7 in conda, do I need to install python 3.5?)

Any help or hint will be very much appreciated.
I have 6 pacbio bacterial genome assemblies I would like to evaluate by using sm_assemblies.

Best reagards,

pomidorku

[mw55309]

Hello!

Indeed Splign cannot be installed through conda.

As long as Splign is in your $PATH, things should work.

Can you install from .tar.gz?

Cheers
Mick

[pomidorku]

Hello,
I was able to reinstall libuv, pcre and liblmdb by using apt install, but outside the environment were I will run sm_assemblies. splign works now in my laptop.

I run the command: snakemake --use conda on all the genomes for the sample run of the pipeline. All the jobs show an error message resembling the one shown below:

[Tue Mar 3 10:08:55 2020]
Finished job 31.
2 of 30 steps (7%) done
needHugeMem: Out of huge memory - request size 134217728 bytes, errno: 12

"[Tue Mar 3 10:09:28 2020]
Error in rule blat:
jobid: 35
output: blat_chm1.round2.psl
shell:
blat genomes/chm1.round2.fasta protein_coding_exons.filtered.fasta -out=blast9 -ooc=chm1.round2.ooc blat_chm1.round2.psl
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job blat since they might be corrupted:
blat_chm1.round2.psl"

My laptop has 16GB ram. I may need a higher RAM capacity for this pipeline to work?

Regards,

pomidoreku

[pomidorku]

Hi,

After having problems running the pipeline, I cloned it again with the updated code from 4 days ago.

Now I get the following error:

"SyntaxError in line 140 of /home/ivapps/sm_assemblies/Snakefile:
No rule keywords allowed after run/shell/script/wrapper/cwl in rule report. (Snakefile, line 140)"

and the job exits with no results at all.

Does the code need to be fixed?

Regards,

pomidorek

[mw55309]

Try now @pomidorku - sorry about that

[mw55309]

I was able to reinstall libuv, pcre and liblmdb by using apt install

Hi, certainly those all appear to be installable with conda:

https://anaconda.org/conda-forge/libuv
https://anaconda.org/anaconda/pcre
https://anaconda.org/anaconda/lmdb

I do apologise for the issues here, splign is not my softare and it is hard for me to debug the installation of this.

And it does indeed look like you may need more RAM

[pomidorku]

Dr. Watson,
The goal of the pipeline is great. Thank you for making it available to the scientific community.
I will try to find a work around for the issues that impede me running this great tool.
Regards,
pomidorku

[pomidorku]

One more question. What perl version is sm_assemblies compatible with?