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bitia
bitia-cli
Commits
2cb3c92c
Commit
2cb3c92c
authored
2 years ago
by
selva
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203cf1a3
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!15
Update Documentation
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#4559
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docs/source/getting_started/Working.md
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2cb3c92c
# WORKING WITH BiTIA
To
L
ist available commands and options in bitia, execute
`bitia --help`
To
l
ist available commands and options in bitia, execute
`bitia --help`
<div
id=
"termynal"
data-termynal
>
<span
data-ty=
"input"
>
python -m bitia --help
</span>
...
...
@@ -58,13 +58,13 @@ Usage: python -m bitia run [OPTIONS] USER_INPUT<br>
The Argument
`user_input`
can be used in three ways:
1.
Executing
C
ommands
1.
Executing
c
ommands
2.
Executing pipelines
3.
Executing
D
irectories with multiple required files
3.
Executing
d
irectories with multiple required files
**1. Executing Commands**
For executing any single task of
B
ioInformatics pipeline, we can instruct Bitia specific single-line commands.
For executing any single task of
b
ioInformatics pipeline, we can instruct Bitia specific single-line commands.
<div
id=
"termynal2"
data-termynal
>
...
...
@@ -76,12 +76,12 @@ The Argument `user_input` can be used in three ways:
The above code will:
-
Checks for the input file
`foo.fa`
in the current working directory
-
Download the input file from
the given link
`http://example.com/foo.fa`
and name it
`foo.fa`
-
Add the
given
command
`samtools convert <foo.fa|http://example.com/foo.fa`
into a pipeline file.
-
Download the input file from
`http://example.com/foo.fa`
and name it
`foo.fa`
-
Add the command
`samtools convert <foo.fa|http://example.com/foo.fa`
into a pipeline file.
-
Extract the current working directory with the pipeline as a zip file that contains a unique hash and send it to the server
`public.bitia.link`
-
The BiTIA runner in the server will execute the pipeline by:
-
Installing the given command
`samtools`
-
Downloading the given input file from
the link
`http://example.com/foo.fa`
and name it
`foo.fa`
-
Downloading the given input file from
`http://example.com/foo.fa`
and name it
`foo.fa`
-
Executing the command
`samtools convert foo.fa`
-
Display the resulting output to the user console
...
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