Open frentzeperis opened 10 months ago
Hi,
I'm also encountering problems when attempting to install SQuIRE. So far, I tried the following alternatives:
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
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
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
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
Any update to this? I attemped to follow @singhbhavya's method and received the same error as @Kiliankleemann.
Hello,
I am trying to set up SQuIRE on my school's hpc cluster but the installation is failing (at: mamba create -n squire -c bioconda squire). I have a new account and have tried conda and mamba create on fresh installations of miniconda 2, miniconda 3, and the most recent anaconda. All of them are failing to create the squire environment with an error that reads some variant of:
Collecting package metadata (current_repodata.json): done Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source. Collecting package metadata (repodata.json): done Solving environment: \ Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed
UnsatisfiableError:
And then I am returned to the command line. Mamba gives bit more detail about which packages conflict but the whole thing is so strange. My local installation of SQuIRE on my MacBook worked fine but this is failing. Do you have any insights?
Best, Frederika