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*Maybe first a stupid question: but do you need to state that for the analysis a UNIX operating system is necessary? I know that this is probably obvious, just wanted to make sure.
*Then I again made some minor text changes (please revise them and revert if you feel they made things worse).
*Specific issues:
   *Line 28-40: I could not install snakemake with the command you provided, probably because my python was too new? I got the following error:

`UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - snakemake==5.2 -> python[version='>=3.5,<3.6.0a0|>=3.6,<3.7.0a0']

Your python: python=3.7'

   *Line 57: I followed the other commands to install majiq, but installation of the last command failed for me. I will try to attach a log file, which might help you (and me) to understand why... at first glance it seems to have a problem with gcc, i.e. with my C compiler and C++ compiler.

   *Line 69: I could not install devtools with the given command. several packages were not available:
' ERROR: dependencies ‘usethis’, ‘covr’, ‘httr’, ‘rversions’ are not available for package ‘devtools’
* removing ‘/home/volker/miniconda3/envs/leafcutter/lib/R/library/devtools’
'

   *Line 87: first of all, you probably need to tell people where to find the "junctionseq.yml", although you point this out at the top, I would probably re-iterate here to make sure people understand. Then, I simply could not run the command:

'(base) volker@gehring-workstation1:~/Tools/baltica/envs$ conda env create -f junctionseq-env.yml --yes
usage: conda-env [-h] {create,export,list,remove,update,config} ...
conda-env: error: unrecognized arguments: --yes
'
Hope those comments help in any way. I would be happy to try to fix those problems. Maybe they are mostly because of issues with my machine...
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boehmv authored Jul 30, 2020
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# Getting started

Baltica comprise of a collection of workflows and analysis scripts. Workflows are powered by [Snakemake](https://snakemake.readthedocs.io/en/stable/) [^1]. Analysis are done with the Rlang. Bellow we document how to obtain install the methods on which Baltica depends.
Baltica is comprised of a collection of workflows and analysis scripts. Workflows are powered by [Snakemake](https://snakemake.readthedocs.io/en/stable/) [^1]. Analysis are done with the Rlang. Below we document how to obtain and install the methods on which Baltica depends.

## Install miniconda

Expand Down Expand Up @@ -66,7 +66,7 @@ conda create --name leafcutter python=2.7 --yes
conda activate leafcutter
conda install -c bioconda samtools r-base=3.6 --yes

Rscript -e "install.packages('devtools', repos='http://cran.us.r-project.org', dependencies=TRUE)"
Rscript -e "install.packages('devtools', repos='http://cran.us.r-project.org',warning dependencies=TRUE)"
Rscript -e "Sys.setenv(TAR = '/bin/tar'); devtools::install_github('stan-dev/rstantools')"
Rscript -e "Sys.setenv(TAR = '/bin/tar'); devtools::install_github('davidaknowles/leafcutter/leafcutter')"
```
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@tbrittoborges tbrittoborges commented on e5e2350 Jul 30, 2020 •
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Maybe first a stupid question:

There is no such thing!

but do you need to state that for the analysis a UNIX operating system is necessary? I know that this is probably obvious, just wanted to make sure.
It's actually not obvious for people how have little experience with the computational side. There are a lot of people trying to use Majiq and Leafcutter in windows PC and Macs. If would be great if these workflow recipes help those people, but I don't know. Also, it's good practice to detail the system/version used for development.
*Then I again made some minor text changes (please revise them and revert if you feel they made things worse).

Thanks.

*Line 28-40: I could not install snakemake with the command you provided, probably because my python was too new? I got the following error:

Indeed. Snakemake needs python ~3.6. I updated the recipe with this detail.

*Line 57: I followed the other commands to install majiq, but installation of the last command failed for me. I will try to attach a log file, which might help you (and me) to understand why... at first glance it seems to have a problem with gcc, i.e. with my C compiler and C++ compiler.

Unfortunately Majiq was never easy to get installed, as it is very problematic and the logs are not helpful at all (this error is kind generic). I will review this recipe.

*Line 69: I could not install devtools with the given command. several packages were not available:

R 4, and some people have updated their packages and some not. It is a double-edge sword because many packages now depend R >4, while others only work with R<3...

*Line 87: first of all, you probably need to tell people where to find the "junctionseq.yml", although you point this out at the top, I would probably re-iterate here to make sure people understand. Then, I simply could not run the command:
conda-env: error: unrecognized arguments: --yes

Fixed.

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