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ISUgenomics / SequelTools

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Conda version #18

Closed JonEilers closed 2 years ago

JonEilers commented 2 years ago

Hi, Just wondering if there are plans to create a conda package for SequelTools?

aseetharam commented 2 years ago

Hi @JonEilers: Thanks for trying SequelTools. The dependencies of SequelTools are very simple (samtools, python, and R), and the program itself is a script that you can execute directly (without compiling). Thus, we think conda package for SequelTools is overkill. If you are interested in creating one, we will be glad to provide the information you need!

Thanks,

JonEilers commented 2 years ago

I agree installation is simple. However, I ran into strange dependency issues. See two different errors below. I never actually figured it why I was getting either of those errors other then removing and creating a new environment and reinstalling the packages eventually solved the problem. It might be helpful to list what specific versions you recommend for those three conda packages? 

SequelTools.sh -p a -n 30 -t Q -u /home/jon/Working_Files/sea_cuke_species_data/stichopus_chloronotus/pacbio/sra/SRR8499556/subFiles.txt
Beginning quality control function

Running in NO_SCRAPS mode
samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/home/jon/Working_Files/sea_cuke_species_data/stichopus_chloronotus/SequelTools/Scripts/generateReadLenStats_noScraps.py", line 107, in <module>
    subMean = Mean(subReadLens)
  File "/home/jon/Working_Files/sea_cuke_species_data/stichopus_chloronotus/SequelTools/Scripts/generateReadLenStats_noScraps.py", line 37, in Mean
    mn = float(sum(listx)) / float(len(listx))
ZeroDivisionError: float division by zero
ERROR: Calculation of read length statistics failed!

and 

SequelTools.sh -p a -n 40 -t Q -u /home/jon/Working_Files/sea_cuke_species_data/stichopus_chloronotus/pacbio/sra/SRR8499555/subFiles.txt
Beginning quality control function

Running in NO_SCRAPS mode
/home/jon/miniconda3/envs/sequeltools/lib/R/bin/exec/R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory
SequelTools has finished!
aseetharam commented 2 years ago

Could you please check your samtools installation? 

samtools --version

The SequelTools need functional samtools in its path for it to work.

Thanks,