Snakemake: I keep getting The 'conda' command is not available in $PATH. when running on SGE cluster
来源： https://stackoverflow.com/questions/49680732/snakemake-i-keep-getting-the-conda-command-is-not-available-in-path-when-ru
environment-modules
How can I use the Environment Modules system in Perl?
来源： https://stackoverflow.com/questions/26786813/how-can-i-use-the-environment-modules-system-in-perl
How can I use the Environment Modules system in Perl?
来源： https://stackoverflow.com/questions/26786813/how-can-i-use-the-environment-modules-system-in-perl
module: command not found
问题 I'm attempting to load several modules for building a library on Linux but am told that the command 'module' doesn't exist. I've Googled around and discovered that the solution was to source a directory called "module" which I am unable to locate despite extensive searching. I'm not quite sure what I should and any help would be appreciated (it might help to know that the makefile I'm working with uses csh while my default shell is bash). Thanks! 回答1: I tried to reproduce it and it turns out
How to issue “module load” in a shell or Perl script (i.e., non-interactively)
问题 I can use the "module load xyz" command interactively, but when run from a script, it says it can't find the "module" command. Is there any way of loading modules in a script? 回答1: Start your bash script like this: #!/bin/bash -l Note that modules loaded after this with module load xyz will only be available from inside the script file. 回答2: Try source /etc/profile If that doesn't work, you most likely have a problem with aliases. You may need shopt -s expand_aliases in your script. 回答3: If
Setting-up Environment Modules
问题 I have recently installed the environment-modules package (version 4.1.1-1 ) on Linux Mint 19, and I'm trying to figure out how to set-up different environments. Unfortunately, the docs only give few pointers as what to do when you're not already an expert on the subject matter (I was hoping for a simple example, instead I found mostly just a list of commands). To be more concrete, I have the following situation: I have Modules installed in /usr/share/modules/ . I have compiled OpenMPI using
How to use environment modules in a ssh command line?
问题 The Environment Modules package is used for dynamic modification of a user's environment ( debian package environment-modules ). I would like to use module directly from a ssh command line. The purpose is to be able to execute commands on different nodes from a bash script executed on a front node. I don't want to explicitly update PATH and LD_LIBRARY_PATH environment variables for each different node configuration. When I directly connect to the node and then call module from the node, it is
Starting module shell command from python subprocess module
问题 I'm trying to run vnc server, but in order to do it first I need to run 'module load vnc'. If I call which module in loaded bash shell then the command in not found is the PATH but in the same time it's available. It looks like the command is built-in. In other words it looks like I need to execute two commands at once module load vnc;vncserver :8080 -localhost and I'm writing script to start it from python. I have tried different variants with subprocess.Popen like subprocess.Popen('module
How to issue “module load” in a shell or Perl script (i.e., non-interactively)
I can use the "module load xyz" command interactively, but when run from a script, it says it can't find the "module" command. Is there any way of loading modules in a script? Start your bash script like this: #!/bin/bash -l Note that modules loaded after this with module load xyz will only be available from inside the script file. Try source /etc/profile If that doesn't work, you most likely have a problem with aliases. You may need shopt -s expand_aliases in your script. If by modules you mean Linux kernel modules, look into modprobe (or the more low-level insmod ). There's usually no need
loading-environment-modules-within-a-python-script
问题 Loading environment modules within a python script The above solution behaves differently in the python interactive shell and within an executable python file & I need some help in understanding how to get it to work in the exe.py setting, where import statements appear not to be seeing the environment variable PYTHONPATH. In python shell the solution allows loading of an environment module which modifies PYTHONPATH; I can subsequently import a python module from that amended PYTHONPATH. This