How to install eclipdemux

[nikou123456]

Hi there,
After downloading files 'eclipdemux', I installed it using the following command

>sudo python setup.py build
>sudo python setup.py. install

When I try to use "eclipdemux" order, there shows no eclipdemux tool on my system. Could you tell me how to install eclipdexmux and how to use it ?
>eclipdemux --help

Best,
Jessica

[FionaMoon]

I meet the same problem.
Anyone can help?

[niekwit]

Hi both,

I run the script without installing it:

(base) niek@desktop:.../scripts$ git clone git@github.com:niekwit/eclipdemux.git
(base) niek@desktop:.../scripts$ python eclipdemux/eclipdemux_package/demux.py --help
Usage: takes raw fastq files and demultiplex inline randomer and adapter sequences

Options:
  -h, --help            show this help message and exit
  --dataset=DATASET     
  --newname=NEWNAME     
  -m METRICSFILE, --metrics=METRICSFILE
  --fastq_1=FASTQ1      fastq file to barcode demux
  --fastq_2=FASTQ2      fastq file to barcode demux
  --expectedbarcodeida=EXPECTEDBARCODEIDA
  --expectedbarcodeidb=EXPECTEDBARCODEIDB
  -b BARCODESFILE, --barcodesfile=BARCODESFILE
                        reference barcodes fasta or tsv file (tsv columns:
                        barcode_sequence/barcode_id)
  --length=RANDOMER_LENGTH
                        Length of randomer sequence at front of 2nd read
  --max_hamming_distance=ALLOWED_DISTANCE
                        Max Hamming distance between read barcode and given
                        barcodes to assign a barcode to a read
  --legacy           

After you have fixed the izip import error (see my fork), you can run the script (Python 3.10.10)

[Phooooebe]

Hi both,

I run the script without installing it:

(base) niek@desktop:.../scripts$ git clone git@github.com:niekwit/eclipdemux.git
(base) niek@desktop:.../scripts$ python eclipdemux/eclipdemux_package/demux.py --help
Usage: takes raw fastq files and demultiplex inline randomer and adapter sequences

Options:
  -h, --help            show this help message and exit
  --dataset=DATASET     
  --newname=NEWNAME     
  -m METRICSFILE, --metrics=METRICSFILE
  --fastq_1=FASTQ1      fastq file to barcode demux
  --fastq_2=FASTQ2      fastq file to barcode demux
  --expectedbarcodeida=EXPECTEDBARCODEIDA
  --expectedbarcodeidb=EXPECTEDBARCODEIDB
  -b BARCODESFILE, --barcodesfile=BARCODESFILE
                        reference barcodes fasta or tsv file (tsv columns:
                        barcode_sequence/barcode_id)
  --length=RANDOMER_LENGTH
                        Length of randomer sequence at front of 2nd read
  --max_hamming_distance=ALLOWED_DISTANCE
                        Max Hamming distance between read barcode and given
                        barcodes to assign a barcode to a read
  --legacy           

After you have fixed the izip import error (see my fork), you can run the script (Python 3.10.10)

so how to fixed the 'izip' import error?