Comments (4)
I understand that those are two different file. I miss-typed and forgot to add filenames. What I was trying to say that those two files have essentially identical name, which they do.
I'm not sure if you've used lmod before https://github.com/TACC/Lmod, but this is fairly common system on alot of the servers and clusters. The two big advantages of using such system:
- Ability to choose different versions of the same tool
- your PATH variable doesn't get populated with every possible tools that had been installed on the system
To be absolutely clear I'm talking about linux OS, in particular I administer ubuntu 14.04 and ubuntu 16.04. I know others using CentOS.
Here is a module wrapper for spades on our system
help(
[[
This module loads spades genome assembler
]])
local base = pathJoin("/mnt/software/apps", "spades-3.10.0-Linux")
local path = pathJoin(base, "bin")
prepend_path("PATH", path)
LmodMessage("Use spades.py instead of spades")
What this does is to append sapdes/bin
into system PATH variable so that spades.py
becomes available in users environment. This is the same for example as putting this into ~/.bashrc
export PATH=/mnt/software/apps/spades-3.10.1-Linux/bin:$PATH
except its better.
Either way sapdes
and spades.py
become available in user's environment. And user have to choose which spades
to run. Do you at lest see that being a little bit of a problem? This is what I was trying to say in my previous message. Not to change content of the file, rather allow users export
bin/
directory and only be presented with one choice of sapdes
On our system I put out a message very time user loads spades
e.g
LmodMessage("Use spades.py instead of spades")
But this seem silly, don't you think?
It is up to you of course whether you want to still think about changing names or other work-arounds or not. I'll leave it with you, but you can't deny that both spades
and sapdes.py
are found in the bin
directory and from user's point of view this is confusing, particular when majority of other bioinformaticky tools are run without a suffix e.g cutadapt
, mimodd
, and multiqc
are all python based tool.
Thanks
from spades.
I'm a bit late here, but I agree that it is confusing to include an executable file called spades
and one called spades.py
in the same folder. Namely, I installed to /usr/local
so SPAdes would be in my PATH
, and both spades
and spades.py
result in my PATH
(even though I should only run spades.py
, not spades
). I think this adds unnecessary confusion
from spades.
Hello
Thank you for your interest in SPAdes.
It's a bit confusing to have essentially indential files in the bin/ directory and both have executable permissions on them
They are not. In particular, spades.py
is a glue script that includes a lot of pipeline logic and spades
is one of the apps of the suite.
The main problem for us is that we use lmod enviromental modules system on our servers and when I module load spades I
This smells like a problem os this system.
Please let me know if you have any temproral fixe for this problem and your long term thought
There are no plans to "fix" this.
from spades.
The binaries now have spades- prefix in the name. SPAdes 3.12 is released.
from spades.
Related Issues (20)
- No error code metaspades just terminate after 13 hours of running kmer counting HOT 3
- spades error #255 unequal amount of reads HOT 1
- SPAdes 4.0.0 incorrect Python version detection? HOT 2
- Python warning on 3.12
- SPAdes: K21,33,55,77,99,127, didtn't generate any data in files: scaffolds.gfa and contigs.fasta HOT 1
- Memory Limitation/ Finished abnormally HOT 1
- 'Failed to limit memory to' error on Mac M3 Max, while SPAdes runs normally via a virtual Linux machine on the same computer. HOT 6
- Build system should use available deps instead of externals when they are available
- SyntaxWarning: invalid escape sequence '\d' return [atoi(c) for c in re.split("(\d+)", text)]
- Anaconda cannot download new version of spades HOT 1
- Creating a Continuous Contig from SPAde Output
- Incompatible licenses HOT 1
- Error == system call for: config.info HOT 4
- Spades finished abnormally HOT 1
- SPAdes: Running since 4 days HOT 4
- Resuming Hybrid Assembly fails HOT 2
- OS return value: -9 HOT 5
- == Error == system call for: spades-core, finished abnormally, OS return value: -9 HOT 1
- Linux build does not run in a directory containing spaces
- Input requirement for hybrid assembly HOT 6
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from spades.