trying to apply to current sequel data : no target/dist/bin/launch in the path

[splaisan]

The doc gives a command example which does not work since the path-to-launch does not exist

target/dist/bin/launch -i path/to/modifications.csv -f path/to/reference.fasta -o output_prefix -b vector_specifier -g gamma -l min_length predict

this 'target/dist/bin/launch' does not exist and when I replace 'target/dist/bin/launch' by 'bin/sbt" I get the message:

AgIn=$BIOTOOLS/AgIn
options="-b ${AgIn}/resource/P6C4.dat -g -0.55 -l 40"

${AgIn}/bin/sbt -i basemods.csv \
        -f reference.fasta \
        -o AgIn \
        ${options} \
        predict

OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=384M; support was removed in 8.0
[info] Set current project to default-4dcdb8 (in build file:/data/NC_projects/yeast_motifs/)
[error] Not a valid key: basemods (similar: streams)
[error] basemods.csv
[error]         ^
[error] Not a valid command: i
[error] Not a valid project ID: i
[error] Expected ':'
[error] Not a valid key: i
[error] i
[error]  ^

replacing by '/src/script/launch' gives another error

Error: Could not find or load main class org.codehaus.plexus.classworlds.launcher.Launcher

Can you please correct the syntax to match your code Thanks in advance

[splaisan]

For others with similar problem and from feedback by the author, it seems that I could not build the app properly because of my recent version of Java. One may try running bin/sbt with an older Java version.

[phlatphish]

Same problem here. Fails with bioconda builds of Java 6.0.77 , 7.0.91 , 8.0.112. Did you get it to run?

For others with similar problem and from feedback by the author, it seems that I could not build the app properly because of my recent version of Java. One may try running bin/sbt with an older Java version.

[hacone]

bin/sbt package-dist must be issued to generate dist/bin/launch... sorry for inconvenience. Let me point out that this project was designed and tested with RSII platform, and does not have appropriate parameters working well with Sequel data currently. I'm planning to upgrade the whole project to catch up with the latest platform and reagents, as there is no reason to expect that the concept expanded here cannot applicable to them. I appreciate your patience.

I think the new version would be written in python.

[splaisan]

Thanks @hacone , we all look forward to this new version. This is a hot topic and tools are scarse to say the least! Best, Stephane

[AmaliT]

Hi @hacone , I was wondering if there is an update on the new version that will be designed to analyse data from sequel system?