homer installation

Question

[leslielebon]

Hi ! I need help please. I am trying to install homer on a unix machine everything goes well until i arrived to the end, i have the message :

‘homer.package.zip’ saved [19312984/19312984]

                Unzipping...
                Finished Installing homer

without end...

this is the complete installation messages

$ perl /software/homer/configureHomer.pl -install

        Current base directory for HOMER is /software/homer/

--2025-01-08 21:09:22--  http://homer.ucsd.edu/homer/update.txt
Resolving homer.ucsd.edu (homer.ucsd.edu)... 169.228.63.226
Connecting to homer.ucsd.edu (homer.ucsd.edu)|169.228.63.226|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 19497 (19K) [text/plain]
Saving to: ‘/software/homer//update.txt’

/sci/home/leslie.cohen/ 100%[============================>]  19.04K  96.9KB/s    in 0.2s

2025-01-08 21:09:23 (96.9 KB/s) - ‘/software/homer//update.txt’ saved [19497/19497]

        Updating Settings...
`wget -O 0.728403723406704.tmp http://homer.ucsd.edu/homer/configureHomer.pl`;
--2025-01-08 21:09:23--  http://homer.ucsd.edu/homer/configureHomer.pl
Resolving homer.ucsd.edu (homer.ucsd.edu)... 169.228.63.226
Connecting to homer.ucsd.edu (homer.ucsd.edu)|169.228.63.226|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 27679 (27K) [application/x-perl]
Saving to: ‘0.728403723406704.tmp’

0.728403723406704.tmp   100%[============================>]  27.03K   139KB/s    in 0.2s

2025-01-08 21:09:23 (139 KB/s) - ‘0.728403723406704.tmp’ saved [27679/27679]

        configureHomer.pl script is up-to-date
        Packages to Install...
                homer ->

        Checking for standard utilities and 3rd party software:

                (Note: seqlogo, gs, and blat no longer required)
        Checking for wget... /usr/bin/wget
        Checking for cut... /usr/bin/cut
        Checking for gcc... /usr/bin/gcc
        Checking for g++... /usr/bin/g++
        Checking for zip... /usr/bin/zip
        Checking for unzip... /usr/bin/unzip
        Checking for make... /usr/bin/make
        Checking for tar... /usr/bin/tar
        Checking for gunzip... /usr/bin/gunzip
        Checking for gzip... /usr/bin/gzip

        All auxilary programs found.

        Pausing for 3 seconds (hit ctrl-C to stop)
        Installing: homer
                Downloading...
--2025-01-08 21:09:26--  http://homer.ucsd.edu/homer/data/software/homer.v5.1.zip
Resolving homer.ucsd.edu (homer.ucsd.edu)... 169.228.63.226
Connecting to homer.ucsd.edu (homer.ucsd.edu)|169.228.63.226|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 33045679 (32M) [application/zip]
Saving to: ‘homer.package.zip’

homer.package.zip       100%[============================>]  31.51M  9.44MB/s    in 3.3s

2025-01-08 21:09:30 (9.44 MB/s) - ‘homer.package.zip’ saved [33045679/33045679]

                Unzipping...
                Finished Installing homer

When I check my homer directory, everything seems to be here except the file config.txt...

I killed the install.

I did exactly what it is said in the website Any idea?

Thanks a lot

[GenoMax]

Have you tried to run homer? Perhaps the config.txt file is made when you run it the first time.

[leslielebon]

I tried but I obtained this error: Could not open configuration file (/software/homer//config.txt)

[GenoMax]

Have you tried this basic configuration method: http://homer.ucsd.edu/homer/introduction/configure.html

According to GPT the format of the file is like follows (so you can make one up, if above does not work):

GENOME: MyCustomGenome
VERSION: v1.0
ORGANISM: Human
SOURCE: Custom Assembly
DATE: 2025-01-06
AUTHOR: Your Name
EMAIL: [e-mail]

# File paths
GENOME_FASTA: /path/to/MyCustomGenome.fasta
CHROM_SIZE: /path/to/MyCustomGenome.chrom.sizes
GENOME_INDEX: /path/to/MyCustomGenome.bowtie.index

# Annotation files (optional but recommended)
GTF_FILE: /path/to/MyCustomGenome.gtf
ANNOTATION_FILE: /path/to/MyCustomGenome.annotation.txt

# Additional options
GENOME_DESCRIPTION: "Custom genome based on a specific assembly."

Also note:

Tips for customizing config.txt

• Ensure paths are absolute or accessible relative to HOMER's working directory.
• Use descriptive names for GENOME and VERSION for easy identification.
• Validate the FASTA file, chromosome size file, and annotations for consistency.