shell script within Conda env can't execute mkdir

We are on an Ubuntu system running conda.
Within an environment (python2, pandas, other packages) we are trying to run a shell script that:
1. creates dir (mkdir)
2. runs executables the path to which are in PATH (.bashrc)

Neither of these are working, and I imagine is a config error on our part.

Here are the errors:

mkdir: cannot create directory ‘ResultsSparCC/Resamplings2’: No such file or directory
mkdir: cannot create directory ‘ResultsSparCC/Bootstraps’: No such file or directory
./sparccWrapper.sh: line 31: ResultsSparCC/sparcc.log: No such file or directory
Traceback (most recent call last):
File "/home/charlesh/binf/src/sparcc/MakeBootstraps.py", line 9, in <module>
from analysis_methods import permute_w_replacement
File "/home/binf/src/sparcc/analysis_methods.py", line 7, in <module>
from pandas import DataFrame as DF
ImportError: No module named pandas


However, pandas is installed in the environment:

$conda list|grep pandas
pandas 0.23.1 py27h637b7d7_0


Here is a snippet of the offending code in the script:

#!/bin/bash
////
INPUT_PATH="foo.txt"
OUTPUT_PATH="ResultsSparCC"
///
mkdir $OUTPUT_PATH/Resamplings2
mkdir $OUTPUT_PATH/Bootstraps


Suggestions?

ResultsSparCC

mkdir -p

1 Answer
1

The main suggestion is: read the error-message.

mkdir: cannot create directory ‘ResultsSparCC/Resamplings2’: No such file or directory


mkdir complains that there is no directory ResultsSparCC in which it should create Resamplings2.

mkdir

ResultsSparCC

Resamplings2

So, if you do ls -l, do you see the directory ResultsSparCC? Probably not. What happens if you do `mkdir ResultsSparCC/Resamplings2’ by hand?

ls -l

ResultsSparCC

If you create the directory ResultsSparCC, all scripts should work.

ResultsSparCC

Alternatively, use mkdir -p:

mkdir -p

#!/bin/bash
#////
INPUT_PATH="foo.txt"
OUTPUT_PATH="ResultsSparCC"
///
mkdir -p $OUTPUT_PATH/Resamplings2
mkdir -p $OUTPUT_PATH/Bootstraps


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