perun_and_environments
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| perun_and_environments [2018/06/27 15:49] – 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 You should always check if the software you need is under conda as an **outdated** version of it may be in the environmental variables of the cluster.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. | ||
| 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 | ||
| 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 77: | Line 81: | ||
| (blast) / | (blast) / | ||
| - | # packages in environment at / | + | # packages in environment at / |
| - | + | #\\ | |
| - | # | + | # Name Version |
| - | + | libgcc | |
| - | # Name Version | + | libgcc-ng |
| - | + | libstdcxx-ng | |
| - | libgcc | + | samblaster |
| - | + | ||
| - | libgcc-ng | + | |
| - | + | ||
| - | 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 | Some of the more common environments you might be interested in | ||
| Line 109: | Line 113: | ||
| source activate busco | source activate busco | ||
| - | So, to run albacore or porechop or nanostat or nanoplot | + | 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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