Unable to Install SQuIRE about squire HOT 3 OPEN

Updating this issue with what worked for me:

I built an empty environment, in which I installed the specified R version.

conda create -n squire
conda activate squire
conda install r-base=3.4.1

I then downloaded SQuIRE from Git, and installed it manually.

git clone https://github.com/wyang17/SQuIRE; cd SQuIRE; pip install -e .

I ran SQuIRE Build

squire Build -s all

I downloaded a few more dependencies based on what was required / as errors popped up:

conda install -c bioconda ucsc-gtftogenepred
conda install -c bioconda ucsc-genepredtogtf
conda install -c bioconda ucsc-bedgraphtobigwig
conda install -c bioconda ucsc-genepredtobed

I ran SQuIRE Fetch, using these commands:

squire Fetch -b hg38 -f -c -r -g -x -p 8 -v

SQuIRE Clean:

squire Clean -b hg38

SQuIRE Map

squire Map -1 [read1.fastq] -2  [read2.fastq] -o [outputfolder] --name [name] -b hg38 --verbosity

SquIRE Count

squire Count -m [mapping_folder]  -o [outputfolder]  -t [tmp] -r 60 -n IFF1 -b hg38 --verbosity

I exported my current conda env (if it's helpful for anyone), and this is what it looks like:

conda env export --from-history 

channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - r-base=3.4.1
  - ucsc-genepredtogtf
  - ucsc-genepredtobed
  - ca-certificates
  - certifi
  - openssl
  - ucsc-gtftogenepred
  - ucsc-bedgraphtobigwig

from squire.

Hi,

I'm also encountering problems when attempting to install SQuIRE. So far, I tried the following alternatives:

1. mamba create -n squire -c bioconda squire; which returns variations of the following:
   Encountered problems while solving.
   Problem: package squire-0.9.9.92-pyhdfd78af_0 requires samtools 1.1, but none of the providers can be installed

2. conda create --name squire.env --override-channels -c iuc -c bioconda -c conda-forge -c defaults -c r python=2.7.13 bioconductor-deseq2=1.16.1 r-base=3.4.1 r-pheatmap bioconductor-vsn bioconductor-biocparallel=1.12.0 r-ggrepel star=2.5.3a bedtools=2.25.0 samtools=1.1 stringtie=1.3.3 igvtools=2.3.93 ucsc-genepredtobed ucsc-gtftogenepred ucsc-genepredtogtf ucsc-bedgraphtobigwig r-hexbin ; which returns:
   UnsatisfiableError: The following specifications were found to be incompatible with each other:
   Output in format: Requested package -> Available versions
   Package PACKAGE_NAME conflicts for:
   (...long list of conflicts...)

Any help would be great! :)
Thank you

Best,
Matteo

from squire.

thanks for the comment @singhbhavya - tried it our but i got the following: Traceback (most recent call last):
File "/home/kilian/miniconda3/bin/squire", line 33, in
sys.exit(load_entry_point('SQuIRE', 'console_scripts', 'squire')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kilian/miniconda3/bin/squire", line 25, in importlib_load_entry_point
return next(matches).load()
^^^^^^^^^^^^^^^^^^^^
File "/home/kilian/miniconda3/lib/python3.11/importlib/metadata/init.py", line 202, in load
module = import_module(match.group('module'))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/kilian/miniconda3/lib/python3.11/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "", line 1204, in _gcd_import
File "", line 1176, in _find_and_load
File "", line 1147, in _find_and_load_unlocked
File "", line 690, in _load_unlocked
File "", line 940, in exec_module
File "", line 241, in _call_with_frames_removed
File "/home/kilian/SQuIRE/squire/cli.py", line 17, in
import Build as s1
File "/home/kilian/SQuIRE/squire/Build.py", line 28
os.makedirs(path, 0770)
^
SyntaxError: leading zeros in decimal integer literals are not permitted; use an 0o prefix for octal integers

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