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AnHo published a blog post How to set up SSH on Ubuntu 18.04Comments- LEGE 1807 days ago
The SSH server is not installed by default on Ubuntu desktop systems but it can be easily installed from the standard Ubuntu repositories.
To install and enable SSH on your Ubuntu system complete the following steps:
Open your terminal either by using the
Ctrl+Alt+Tkeyboard shortcut or by clicking on the terminal icon and install theopenssh-serverpackage by typing:sudo apt updatesudo apt install openssh-serverOnce the installation is completed, the SSH service will start automatically. To verify that the installation was successful and SSH service is running type the following command which will print the SSH server status:
sudo systemctl status sshUbuntu comes with a firewall configuration tool called UFW. If the firewall is enabled on your system, make sure to open the SSH port:
sudo ufw allow sshOnce you’ve found the IP address, login to remote machine by running the following
sshcommand:ssh user@ipIf you don’t know your IP address you can easily find it using the this
ip a
- Jitendra Narayan is now a friend with AnHo
- AnHo is now a friend with Jitendra Narayan
- Rahul Nayak posted to the wire
- Neel published a blog post List of motif discovery tools !Comments
- Jit 2232 days ago
Motif algorithms
This link on Nature explain: how does DNA sequence motif discovery work?
Paper on BMC bioinformatics: survey of DNA motif finding algorithms
This paper discusses some limitations and potentials of motif discovery algorithms (2005)
- Jit 2232 days ago
Bioinformatics for Beginners https://www.coursera.org/learn/bioinformatics which can help with learning the basics of the algorithms underpinning motif discovery.
- BioStar published a news post NCBI to assist in Virus Hunting Data Science Hackathon
- Abhimanyu Singh posted to the wire
- Rahul Nayak posted to the wire
- Neel commented on a bookmark List of Bioinformatics Vacancy, Jobs, Opportunity websites
- Neel bookmarked ASCIIGenome: genome browser based on command line interface and designed for running from console...Comments
- Jit 1771 days ago
This a list of available commands with their brief description.
For help on individual commands use one of::
command -h
?command
help command
e.g. `ylim -h`
N a v i g a t i o n
goto chrom:[from]-[to]
Go to region `chrom:from-to` or to `chrom:from` or to the start of
`chrom`.
INT from [c | to]
Go to position `from` or to region `from to` on current chromosome.
PERCENT from [c | to]
Zoom into the current window delimited by given PERCENT of screen.
+ INT [k|m]
Move forward by `INT` bases. Suffix K/M recognized.
- INT [k|m]
Move backwards by INT bases. Suffix K/M recognized.
f [NUM=0.1]
Move forward NUM times the size of the current window, 1/10 by default.
b [NUM=0.1]
Move backward NUM times the size of the current window, 1/10 by default
ff
Move forward by 1/2 of a window. A shortcut for `f 0.5`
bb
Move backward by 1/2 of a window. A shortcut for `b 0.5`
zi [INT = 1]
Zoom in INT times. Each zoom halves the window size.
zo [INT = 1]
Zoom out INT times. Each zoom doubles the window size.
extend [mid|window] [INT left] [INT right]
Extend the current window by `INT` bases left and right.
l
Go to the Left half of the current window.
r
Go to the Right half of the current window.
p
Go to the previous visited position.
n
Go to the next visited position.
next [-back] [-start] [-zo INT=5] [track]
Move to the next feature not overlapping the current coordinates.
F i n d
find [-all] [-c] [-F] regex [track]
Find the first record in `track` containing `regex`.
seqRegex [-iupac] [-c] [regex]
Find regex in reference sequence and show matches as an additional
track.
bookmark [-d] [-n name] [-print] [> file] [chrom:from-to]
Creates a track to save positions of interest.
D i s p l a y
grep [-i = .*] [-e = ''] [-c] [-F] [-v] [track_regex = .*]...
Similar to grep command, filter for features including or excluding
patterns.
awk [-off ...] [-F sep_re] [-v VAR=var] [-V] '<script>' [track_regex = .*]...
Advanced feature filtering using awk syntax.
featureColorForRegex [-r/-R regex color] [-v] [track_regex = .*]...
Set colour for features captured by regex.
featureDisplayMode [-expanded | -collapsed | -oneline] [-v] [track_regex = .*]...
Set how annotation features should be displayed.
gap [-on | -off] [-v] [track_regex = .*]...
Display features with or without a separating gap.
gffNameAttr [attribute_name = NULL | -na] [-v] [track_regex = .*]...
GTF/GFF attribute to set the feature name or `-na` to suppress name.
trackHeight [-v] INT [track_regex = .*]...
Set track height to INT lines of text for all tracks matching regexes.
ylim [-v] <NUM|min|na> <NUM|min|na> [track_regex = .*]...
Set the y-axis limit for all tracks matched by regexes.
colorTrack [-v] color [track_regex = .*]...
Set colour for tracks matched by regex.
hideTitle [-on | -off] [-v] [track_regex = .*]...
Set the display of the title line matched by track_regex.
genotype [-n 10] [-s .*] [-r pattern rplc] [-f expr] [-v] [track_regex = .*]...
Customise the genotype rows printed under the VCF tracks.
editNames [-t] [-v] <pattern> <replacement> [track_re=.*]...
Edit track names by substituting regex pattern with replacement.
dataCol [-v] [index = 4] [track_regex = .*]...
Select data column for bedgraph tracks containing regex.
print [-n INT] [-full] [-off] [-round INT] [-hl re] [-esf] [-v] [-sys CMD] [track_regex = .*]... [>|>> file]
Print lines for the tracks matched by `track_regex`.
A l i g n m e n t s
readsAsPairs [-on | -off] [-v] [track_regex = .*]...
Show SAM records as pairs.
filterVariantReads [-r from/to] [-all] [-v] [track_regex = .*]...
Filter reads containing a variant in the given interval.
rpm [-on | -off] [-v] [track_regex = .*]
Set display to reads per million for BAM and TDF files.
samtools [-f INT=0] [-F INT=4] [-q INT=0] [-v] [track_re = .*] ...
Apply samtools filters to alignment tracks captured by the list of
track regexes.
BSseq [-on | -off] [-v] [track_regex = .*]...
Set bisulfite mode for read tracks matched by regex.
G e n e r a l
setGenome fasta|bam|genome
Set genome and reference sequence.
setConfig <file|tag> | <key> <value>
Set configuration arguments.
explainSamFlag INT [INT ...]
Explain the list of bitwise SAM flags.
show <arg>
Show or set features to display.
recentlyOpened [-grep = .*]
List recently opened files.   - Rahul Nayak 1771 days ago
Install ASCIIGenome with conda
(base) [wsu29@bladeamd-2 ~]$ conda install ASCIIGenome
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /data/sata_data/workshop/wsu29/miniconda3
added / updated specs:
- asciigenome
The following packages will be downloaded:
package | build
---------------------------|-----------------
asciigenome-1.15.0 | 0 27.5 MB bioconda
openjdk-8.0.152 | h7b6447c_3 57.4 MB
------------------------------------------------------------
Total: 84.9 MB
The following NEW packages will be INSTALLED:
asciigenome bioconda/noarch::asciigenome-1.15.0-0
openjdk pkgs/main/linux-64::openjdk-8.0.152-h7b6447c_3
Proceed ([y]/n)? y
Downloading and Extracting Packages
openjdk-8.0.152 | 57.4 MB | ################################################################################### | 100%
asciigenome-1.15.0 | 27.5 MB | ################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
