I have created a function configure_propeties() in configure.py that I'm trying to call in a bash script using the following command:
python3.6 -c "import configure; print configure.configure_properties()"
After executing the the bash script I get the following warning:
warning
Both the script and configure.py are in the same directory. Not sure what's happening it doesn't seem to fail on the import. Has anyone seen this issue before?
print "blabla" its only available in python 2, with python 3 you have to use parentheses print("blabla"), it would be better to set your python script inside .py file, just make sure the python executable is in your PATH environment variable then add in your script
python3 path/to/the/python_script.py
In the bash script file bashFile.sh, put this :
#!/bin/bash
python3 path/to/the/python_script.py
then you can execute your bash file bashFile.sh :
bash path/to/bashFile.sh
Use parentheses for print, as is necessary for Python 3
Related
I´m currently writing a snakemake pipeline, for which I want to include a perl script.
The script is not written by me, but from a github page. I never worked with perl before.
I installed perl (5.32.1) via conda. I have installed miniconda and am working on my universities unix server.
The code for my perl script rule looks like this:
rule r1_filter5end:
input:
config["arima_mapping"] + "unprocessed_bam/{sample}_R1.sam"
output:
config["arima_mapping"] + "filtered_bam/{sample}_R1.bam"
params:
conda:
"../envs/arima_mapping.yaml"
log:
config["logs"] + "arima_mapping/r1_filter5end/{sample}_R1.log"
threads:
12
shell:
"samtools view --threads {threads} -h {input} -b | perl ../scripts/filter_five_end.pl | samtools -b -o {output} 2> log"
When I run this I receive the following error:
Can't open perl script "../scripts/filter_five_end.pl": no such file
or directory found
From what I learned while researching is that the 1. line of a perl script sets the path to my perl executable. The script I downloaded had the following path:
#!/usr/bin/perl
And since I use perl installed via conda this is probably wrong. So I set the path to:
#!/home/mi/my_user/miniconda3/bin/perl
However this did still not work, regardless of if I call
perl ../scripts/filter_five_end.pl
or
../scripts/filter_five_end.pl
Maybe it´s just not possible to run perl scripts via snakemake?
Anyone who had encountered this specific similar case?^^
The problem is not with the shebang. The interpreter path in the shebang doesn't matter because you're calling it with perl ../path directly. The shell that this command is executed in will resolve the path to the perl program (which is very likely the conda one) and then run the script, only taking flags (like -T or -w) from the shebang inside the script.
The error message means it cannot find the actual script file. I suspect when you run that shell command, it's in the wrong directory. Try a fully qualified path.
As stated by OP in their comment:
I forgot that snakemake always looks files up from the Snakemake file not the directory the rules are saved in.
Not quite an answer but perhaps relevant:
I forgot that snakemake always looks files up from the Snakemake file not the directory the rules are saved in.
This is not entirely correct, I think. The reference point is the directory set by -d/--directory which by default is where you execute snakemake:
--directory DIR, -d DIR
Specify working directory (relative paths in the snakefile will use this as their origin). (default: None)
I want to call the make command from a bash script in a MinGW bash shell. However the script seems to know "make" only when I call the script using source:
build.sh:
#!/bin/bash
make all
Calling
source build.sh
from the terminal works: The target all is built.
Calling only
build.sh
from the terminal results in
./build.sh: line 2: make: command not found
Why do I have to source the script to have a working make command?
I own the licensed version of Pycharm. I have installed BashSupport plugin as well.
However, I am not sure what steps are required to remotely test and execute a bash script on RHEL server.
I am able to configure a remote interpreter but the interpreter path is /usr/bin/python.
In my logic you need to change interpreter path to /bin/bash instead of /usr/bin/python or i don't understand what you are trying to do..
I've met the save problem today.
If I use the default pycharm bash configuration, I'll get the following error:
C:\windows\system32\bash.exe C:/git/NewProject/run.sh
/bin/bash: C:/git/NewProject/run.sh: No such file or directory
Process finished with exit code 127
So, I change the default Windows Script path to Linux absolute Script path as following:
Run successfully.
You gotta check the path on server, If there is alias set, You can check alias
$ which python
$ whence python (Some version)
$ ls -l `which python`
I'm trying to get a script running. Essentially I need to load some modules and then execute a python script. So something like this...
#!/usr/bin/env bash
module use /PATH/TO/MODULEFILE
module load MY_MODULE
python my_script.py
The problem that I get is that every time I try to execute the script I get this error - "module: command not found". I don't understand how to change the script to fix this. I am able to run the module command from the shell. I also ran "whereis -b module" and I just got "module:".
What do I need to do to get this module loaded from inside the script? Thanks
You can enable the module command from your python script by sourcing the python.py initialization script provided in the init directory of the Modules installation.
Following piece of python code defines module function, then enables a modulepath and load a modulefile:
#!/usr/bin/python
import os
exec(open('/PATH/TO/MODULES/init/python.py').read())
module('use', '/PATH/TO/MODULEFILE')
module('load', 'MY_MODULE')
If you want to enable the module within your bash script, it could be as simple as using a different command to run the script. For me, running a script script.sh as . script.sh or as ./script.sh will correctly load the module, but running it as sh script.sh will lead to the error you described above.
I tried activating a VirtualEnv through a shell script like the one below but it doesn't seem to work,
#!/bin/sh
source ~/.virtualenvs/pinax-env/bin/activate
I get the following error
$ sh virtualenv_activate.sh
virtualenv_activate.sh: 2: source: not found
but if I enter the same command on terminal it seems to work
$ source ~/.virtualenvs/pinax-env/bin/activate
(pinax-env)gautam#Aspirebuntu:$
So I changed the shell script to
#!/bin/bash
source ~/.virtualenvs/pinax-env/bin/activate
as suggested and used
$ bash virtualenv_activate.sh
gautam#Aspirebuntu:$
to run the script .
That doesn't throw an error but neither does that activate the virtual env
So any suggestion on how to solve this problem ?
PS : I am using Ubuntu 11.04
TLDR
Must run the .sh script with source instead of the script solely
source your-script.sh
and not
your-script.sh
Details
sh is not the same as bash (although some systems simply link sh to bash, so running sh actually runs bash). You can think of sh as a watered down version of bash. One thing that bash has that sh does not is the "source" command. This is why you're getting that error... source runs fine in your bash shell. But when you start your script using sh, you run the script in an shell in a subprocess. Since that script is running in sh, "source" is not found.
The solution is to run the script in bash instead. Change the first line to...
#!/bin/bash
Then run with...
./virtualenv_activate.sh
...or...
/bin/bash virtualenv_activate.sh
Edit:
If you want the activation of the virtualenv to change the shell that you call the script from, you need to use the "source" or "dot operator". This ensures that the script is run in the current shell (and therefore changes the current environment)...
source virtualenv_activate.sh
...or...
. virtualenv_activate.sh
As a side note, this is why virtualenv always says you need to use "source" to run it's activate script.
source is an builtin shell command in bash, and is not available in sh. If i remember correctly then virtual env does a lot of path and environment variables manipulation. Even running it as bash virtualenv_blah.sh wont work since this will simply create the environment inside the sub-shell.
Try . virtualenv_activate.sh or source virtualenv_activate.sh this basically gets the script to run in your current environment and all the environment variables modified by virtualenv's activate will be available.
HTH.
Edit: Here is a link that might help - http://ss64.com/bash/period.html
On Mac OS X your proposals seems not working.
I have done it this way. I'am not very happy with solution, but share it anyway here and hope, that maybe somebody will suggest the better one:
In activate.sh I have
echo 'source /Users/andi/.virtualenvs/data_science/bin/activate'
I give execution permissions by: chmod +x activate.sh
And I execute this way:
`./activate.sh`
Notice that there are paranthesis in form of ASCII code 96 = ` ( Grave accent )
For me best way work as below.
Create start-my-py-software.sh and pest below code
#!/bin/bash
source "/home/snippetbucket.com/source/AIML-Server-CloudPlatform/bin/activate"
python --version
python /home/snippetbucket.com/source/AIML-Server-CloudPlatform/main.py
Give file permission to run like below.
chmod +x start-my-py-software.sh
Now run like below
.start-my-py-software.sh
and that's it, start my python based server or any other code.
ubuntu #18.0
In my case, Ubuntu 16.04, the methods above didn't worked well or it needs much works.
I just made a link of 'activate' script file and copy it to home folder(or $PATH accessible folder) and renamed it simple one like 'actai'.
Then in a terminal, just call 'source actai'. It worked!