genomiqueens / eoulsan Goto Github PK

Hi, I have tried to used sample dataset according to the eoulsan tutorial. However, I got an error like this:
=== Eoulsan Error ===
java.io.IOException: com.spotify.docker.client.DockerException: java.util.concurrent.ExecutionException: com.spotify.docker.client.shaded.javax.ws.rs.ProcessingException: java.io.IOException: No such file or directory. I suspect this java.io.IOException is not in eoulsan package. Can anyone tell me how to fix it. Thanks.

Hi, I am new to bioinformatics. I have 10X genomic scRNA data and want to use eoulsan to analyze. I have read the tutorials of eoulsan and not sure about the annotation file preparation for eoulsan. I want to use hg19 version for annotation. So far, I have hg19.gtf file and I am wondering if the .gff and .tsv file is also compulsory. I have find a approach to convert .gtf to gff file. However, I don't know where I can get the .tsv file for annotation. Can you guys give me any suggestion. Many thanks.

Hi,

I have tried to follow the 10x Genomics tutorial on my own data. However, when trying to run the analysis I get the following error:

=== Eoulsan Error ===
Error while executing eoulsan: Requirement for step "step12singlecellexperiment" is not available: path

I once also got similar error for "step7multiqc". I looked around, but I couldn't find out what could be the cause of the issue or how to fix it. Could anyone help me?

I'm trying to run eoulsan without using docker, if that makes a difference.

Thanks!

The mapping step can only use one fastq file and there is no parameters refer to PE in Map reads module. It seems that eoulsan doesn't support the PE data?

Hi,

I organize a workshop about conda in two weeks and an attendee gives the eoulsan package as an example to build a conda package. I saw a recipe exists on bioconda but it's not exactly how I want to make it. I prefer to let maven compiles the project for a given platform.

So eoulsan compiles well on windows. I wrote a batch file to call it. The only problem that remains is that I have the following error

Error: The info of eoulsan is not available for your platform. Required platforms: Linux/x86_64, Linux/amd64.

Is it a limitation of your package because you didn't test it on windows or is it because some dependencies are not available on windows ?

Just to know if I continue the conda recipe or not.

when I ran eoulsan.sh I just got this:
./eoulsan.sh: line 97: java: command not found

What should I do?

Hi,

I am using Eoulsan 2.5 and noticed using htop that in the starindexgenerator module, STAR (2.7.8a) was run with --runThreadN 56, which is the maximum available threads on the machine, even if my workflow file is specifying 32:

    <globals>
        <parameter>
                <name>main.local.threads</name>
                <value>32</value>
        </parameter>
    </globals>

The rest of the steps seem to follow the number of threads specified in the XML file.

Please tell me if you need more details about this issue.

Thanks!

[fuwei@genebang eoulsan.bak]$hadoop jar /its1/GB_BT2/fuwei/opt/eoulsan.bak/eoulsan-2.0-beta4/eoulsan-2.0-beta4-e85fecb4.jar execjarhadoop hdfs://XXX/test/workflow-hadoop.xml hdfs://XXXX/test/design.txt hdfs://XXXX/test
16/08/26 16:23:03 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
=== Eoulsan Error ===
Error while executing eoulsan: java.io.IOException: Unable to create directory file:/test/eoulsan-20160826-162303 for log file:file:/test/eoulsan-20160826-162303/eoulsan.log