How to...

Matt

How to fix the error "FATAL: container creation failed:" "error: can't mount image " "failed to mount squashfs filesystem: input/output error":

#This occurs when you try to run a singularity container within a VM and it is located on a mounted ntfs filesystem. The solution is to transfer the container to a different filesystem eg. ext3.

Matt

How to run docker-compose when you get the errors:

File "posixpath.py", line 376, in abspath
FileNotFoundError: [Errno 2] No such file or directory

Open a new terminal and repeat the command.

Matt

How to login to root account in a new ubuntu/xubuntu virtual machine that has been set up with a non-administrator account:

su
yourpasswordfortheuseraccount

Matt

How to update apt and install filezilla on xubuntu using a proxy:

sudo apt -o Acquire::http::proxy="http://user:password@host:port/" update
sudo apt -o Acquire::http::proxy="http://user:password@host:port/" install filezilla

Matt

How to install ubuntu on windows:

Follow the instructions at:
https://s1gr1d.medium.com/how-to-set-up-linux-on-windows-with-wsl-2-debe2a64d20d
(NB. these instructions work for Windows 10 and 11 although the location of the Settings menus may differ slightly. Also note that VMX is the same as VT-X in the BIOS settings)
In Windows Powershell, you may also need to issue the following commands:

bcdedit /set hypervisorlaunchtype Auto
wsl --update

Matt

How to use your phone as a webcam:

https://www.youtube.com/watch?v=ArVDKf2QK1s

Matt

How to fix the following error in NextFlow:

WARN: Failed to render DAG file:

This error prevents NextFlow from drawing the DAG for the pipeline.

#install Graphviz 
#eg. with conda
conda install -c conda-forge graphviz

Matt

How to gather and group all tuple elements in a NextFlow channel by the first and second indexes of each tuple, perform a process on a file containing the first and second indices, and then reform the original channel by scattering:

hc_ch = Channel.of(
    ['abc', 1, file('file1.txt')],
    ['abc', 1, file('file2.txt')],
    ['abc', 1, file('file3.txt')],
    ['def', 2, file('file4.txt')]
)

combinedChannel = hc_ch.groupTuple(by: [0, 1])

Expected structure of combinedChannel:

[ ['abc', 1, [file('file1.txt'), file('file2.txt'), file('file3.txt')]],
['def', 2, [file('file4.txt')]]
]


process delete_txt {

    input:
    tuple val(id), val(sub_id), val(files) from combinedChannel

    output:
    tuple val(id), val(sub_id), val(files) into processedChannel

    script:
    """
    rm ${id}_${sub_id}.txt
    """
}

Expected structure of processedChannel:

[ ['abc', 1, [file('file1.txt'), file('file2.txt'), file('file3.txt')]],
['def', 2, [file('file4.txt')]]
]

flattenedChannel = processedChannel.flatMap { id, sub_id, files -> files.collect { [id, sub_id, it] } }

Expected structure of flattenedChannel:
[ ['abc', 1, file('file1.txt')],
['abc', 1, file('file2.txt')],
['abc', 1, file('file3.txt')],
['def', 2, file('file4.txt')]
]

Matt

How to get the path for the folder containing a bash script within the bash script:

# Get the directory where the script resides
SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
echo $SCRIPTDIR

Matt

How to convert a minimap2 alignment to gff/gtf:
https://github.com/lh3/minimap2/issues/455
https://github.com/lh3/minimap2/files/9591008/bam2gff_fixGffread.zip
bam2gff_fixGffread.zip

minimap2 -t 10 -ax splice:hq -uf ref.fa cdna.fa |/Bio/bin/samtools-1.14 view -b > minimap2.tr.bam
perl bam2gff.pl -b minimap2.tr.bam -o minimap2.tr.gff -s /Bio/bin/samtools-1.14 gffread minimap2.tr.gff -T -o minimap2.tr.gtf
perl fixGffread.pl -i minimap2.tr.gtf -o minimap2.tr.fix.gtf

Alternative method:

#Align sequences and convert to BAM
minimap2 -ax splice --cs target.fa query.fa | samtools sort -O BAM - > alignments.bam
#Convert to BED12 using BEDtools
bedtools bamtobed -bed12 -i alignments.bam > alignments.bed 
#Convert to genePred using UCSC tools
bedToGenePred alignments.bed alignments.genepred
#Convert to GTF2 using UCSC tools. genePredToGtf has additional options that might be useful in specific use cases.
genePredToGtf "file" alignments.genepred alignments.gtf

Matt

How to do a dotplot with minimap2:

minimap2 -DP ref.fa query.fa|miniasm/minidot - > dot.eps