Commit 441d694b authored by Eric CHARPENTIER's avatar Eric CHARPENTIER 🐍
Browse files

updated README with troubleshooting for PS1 unbound variable bug

parent 88b5728f
......@@ -24,6 +24,35 @@ The only requirement is to have a working install of [conda](https://www.anacond
All tools necessary to run the pipeline are described in two conda environment files.
The species specific resources files have to be downloaded manually if not human.
Troubleshooting
---------------
Since conda 4.6, you may have some problems due to the way we source rnaDE environment in Snakefile.
If you get the following error:
```
$HOME/miniconda3/etc/profile.d/conda.sh: line 26: PS1: unbound variable
```
You can apply the solution described at https://github.com/conda/conda/issues/8186 on function `__conda_activate()` and `__conda_reactivate()` in `$HOME/miniconda3/etc/profile.d/conda.sh`.
You can also have this problem with `binutils_linux`, `gcc_linux`, `gfortran_linux`, `gxx_linux`:
```
$HOME/miniconda3/envs/dgeDE/etc/conda/activate.d/activate-binutils_linux-64.sh: line 67: ADDR2LINE : unbound variable
$HOME/miniconda3/envs/dgeDE/etc/conda/activate.d/activate-gcc_linux-64.sh: line 109: SYS_SYSROOT : unbound variable
$HOME/miniconda3/envs/dgeDE/etc/conda/activate.d/activate-gcc_linux-64.sh: line 67: CPPFLAGS : unbound variable
$HOME/miniconda3/envs/dgeDE/etc/conda/activate.d/activate-gfortran_linux-64.sh: line 67: GFORTRAN : unbound variable
$HOME/miniconda3/envs/dgeDE/etc/conda/activate.d/activate-gxx_linux-64.sh: line 67: GFORTRAN : unbound variable
```
You can fix it by adapting the previous trick on the problematic lines (e.g. line 67 `eval oldval="\$${from}$thing"` becomes `eval oldval="\${${from}$thing:-}"` and so on)
Note that if the following error with `CMAKE_PREFIX_PATH_USED` appends in `activate-gcc_linux-64.sh` the corresponding line can be removed.
```
$HOME/miniconda3/envs/rnaDE/etc/conda/activate.d/activate-gcc_linux-64.sh: line 141: CMAKE_PREFIX_PATH_USED : unbound variable
```
Also note that editing thoses files directly will impact all environments using the same version of the package (as conda use hard links when installing an env). Please move the original file as backup file and do modifications on a copy.
### Cloning the repository
```bash
......@@ -143,4 +172,4 @@ cd RNAseq_quantif_pipeline
./install_dependencies.sh
source activate rna
snakemake --config proj="CONFIG/project.json" conf="CONFIG/config.json" --cluster "qsub -e ./logs/ -o ./logs/" -j 30 --jobscript sge.sh --latency-wait 100 -rp
```
\ No newline at end of file
```
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