perun_and_environments
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| perun_and_environments [2018/06/27 15:31] – 129.173.90.41 | perun_and_environments [2018/12/12 11:06] (current) – 129.173.90.41 | ||
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| - | Using environments on perun | + | ====== |
| + | |||
| + | Below you will find the instructions about how to find and run software **IF it is under CONDA**. You should always check if the software you need is under conda as an **outdated** version of it may be in the environmental variables of the cluster. Since not all software available in perun can be run under an environment there are other places where you could check **[[other_software_locations|]]** and if your software requires databases check **[[databases_locations|]]**. | ||
| Perun has conda installed. | Perun has conda installed. | ||
| - | Conda is a package and environment management system. | + | Conda is a package and environment management system.\\ |
| - | Conda installs, runs, and updates packages and their dependencies. | + | Conda installs, runs, and updates packages and their dependencies.\\ |
| Conda creates, saves, loads and switches between environments. | Conda creates, saves, loads and switches between environments. | ||
| Line 9: | Line 11: | ||
| - | '' | + | '' |
| To see the list of all the environments on perun (it is very long!) | To see the list of all the environments on perun (it is very long!) | ||
| - | '' | + | '' |
| The output should look like this at the top | The output should look like this at the top | ||
| - | # conda environments: | + | # conda environments: |
| - | # | + | #\\ |
| - | base * / | + | base * / |
| - | 2pg_cartesian | + | 2pg_cartesian |
| - | Quast-python2 | + | Quast-python2 |
| - | Subread | + | Subread |
| - | Tophat | + | Tophat |
| - | Transdecoder | + | Transdecoder |
| - | Trimal | + | Trimal |
| - | Trinotate | + | Trinotate |
| - | Unicycler-python3 | + | Unicycler-python3 |
| The active environment is the one with an asterisk | The active environment is the one with an asterisk | ||
| Line 33: | Line 35: | ||
| To search the list you can do something like this | To search the list you can do something like this | ||
| - | **'' | + | '' |
| + | or\\ | ||
| + | '' | ||
| - | This will provide you with all the environments with the string blast in them | + | This will provide you with all the environments with the string blast in them\\ |
| - | blast | + | blast |
| - | blast-legacy | + | blast-legacy |
| - | blastalign | + | blastalign |
| - | blastbesties | + | blastbesties |
| - | crb-blast | + | crb-blast |
| - | genblasta | + | genblasta |
| - | genblastg | + | genblastg |
| - | hs-blastn | + | hs-blastn |
| - | igblast | + | igblast |
| - | nanoblaster | + | nanoblaster |
| - | rmblast | + | rmblast |
| - | samblaster | + | samblaster |
| - | ucsc-blasttopsl | + | ucsc-blasttopsl |
| Line 57: | Line 61: | ||
| So | So | ||
| - | '' | + | '' |
| will place your session in the blast environment. | will place your session in the blast environment. | ||
| - | You will notice that the prompt has changed to include the name of the environment like so | + | You will notice that the prompt has changed to include the name of the environment like so |
| (blast) / | (blast) / | ||
| Line 75: | Line 80: | ||
| (blast) / | (blast) / | ||
| - | # packages in environment at / | + | |
| - | # | + | # packages in environment at / |
| - | # Name Version | + | #\\ |
| - | libgcc | + | # Name Version |
| - | libgcc-ng | + | libgcc |
| - | libstdcxx-ng | + | libgcc-ng |
| - | samblaster | + | libstdcxx-ng |
| + | samblaster | ||
| SO, | SO, | ||
| - | to invoke an environment in a qsub shell | + | to invoke an environment in a qsub shell: |
| + | ----------------------------------------------------------------- | ||
| + | '' | ||
| + | '' | ||
| + | '' | ||
| + | '' | ||
| + | '' | ||
| + | '' | ||
| + | '' | ||
| + | '' | ||
| + | ------------------------------------------------------------------ | ||
| + | |||
| + | Some of the more common environments you might be interested in | ||
| + | |||
| + | source activate python36-generic | ||
| + | source activate rseqc+flye-python2 (flye)\\ | ||
| + | source activate python27-generic (ABruijn) \\ | ||
| + | source activate Unicycler-python3 (unicycler) \\ | ||
| + | source activate smartdenovo-python2 (smartdenovo) \\ | ||
| + | source activate nanopolish-python3 (nanopolish)\\ | ||
| + | source activate canu-python3 (canu)\\ | ||
| + | source activate busco | ||
| + | |||
| + | SO, before | ||
| + | |||
| + | '' | ||
| + | |||
| + | **You are already in the environment and do not know what to do next**\\ | ||
| + | |||
| + | 1- invoke the executable command (see your software manual).\\ | ||
| + | |||
| + | 2- if no manual is available and you still don't know what executable to call:\\ | ||
| + | |||
| + | **let' | ||
| + | conda env list|grep ' | ||
| + | | ||
| + | ls / | ||
| + | then select your executable and directly invoke it within the environment: | ||
| + | | ||
| - | '' | ||
| - | '' | ||
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