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Creating the AMI for the evomics.org Workshops

Shell 8.23% Perl 91.12% R 0.65%

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sophies9 konradpaszkiewicz brianjohnhaas exeter-data-analytics

evomics_2017's Issues

gatb: command not found

gatb - either not installed or not in /usr/bin

radseq

For some reason the current radseq install won't recognise hashed passwords in config files. I am sure I had had this working at some point...!?

Perhaps I can add passwords to an ansible vault and import from there during install...

fastq-dump

it's in software but not in path..also needs a download/install task...

qiime 1 env install - reinstall

If qiime 1 env installs are already installed the playbook will fail at trying to reinstall

IGV download path

IGV download path has changed so software_task file needs to be changed to:

# IGV is licensed, please register
# you should register here https://www.broadinstitute.org/software/igv/?q=registration
- name: Downloading IGV {{version}}
  get_url: url="http://data.broadinstitute.org/igv/projects/downloads/{{sub}}/IGV_{{version}}.zip" dest="{{source_dir}}/IGV_{{version}}.zip"

- name: Uncompressing IGV
  unarchive: 
    src="{{source_dir}}/IGV_{{version}}.zip"
    dest="{{software_dir}}"
    copy=no
    creates="{{software_dir}}/IGV_{{version}}/igv.sh"
    
- name: Installing IGV
  file: src="{{software_dir}}/IGV_{{version}}/igv.sh" dest=/usr/local/bin/igv.sh state=link

And the main_software.yaml needs the addition of a new variable called sub.

NOTE - igvtools is no longer in this download folder so this software_task is also broken but I don't need it so not searched for it.

can't load Krona on MAC OS

Get an error message

"install_MAC.app is damaged and can't be opened. You should move it to the Trash."

Any help?

Samtools version hardcorded in software_task

Samtools version is hardcoded in evomics_2017/genomics/software_tasks/samtools.yaml

Rstudio versions need updating

QIIME1 Install from Conda Failing

With following error message:
TASK [Install QIIME 1 from Conda] ****************************************************
fatal: [localhost]: FAILED! => {"msg": "The conditional check 'qiime1_env_installed.stat.exists == false' failed. The error was: error while evaluating conditional (qiime1_env_installed.stat.exists == false): 'qiime1_env_installed' is undefined\n\nThe error appears to have been in '/home/ubuntu/evomics_2017/genomics/software_tasks/qiime_env.yaml': line 5, column 3, but may\nbe elsewhere in the file depending on the exact syntax problem.\n\nThe offending line appears to be:\n\n\n- name: Install QIIME 1 from Conda\n ^ here\n"}
to retry, use: --limit @/home/ubuntu/evomics_2017/genomics/main_software.retry

krona

krona install makes dandling links to github dir rather than the software dir...

tbl2asn version 24.3 needed

Prokka error as current version of tbl2asn is version 20.0.

[15:50:24] Looking for 'tbl2asn' - found /usr/bin/tbl2asn
[15:50:24] Determined tbl2asn version is 20.0
[15:50:24] Prokka needs tbl2asn 24.3 or higher. Please upgrade and try again.

poretools does not compile

loads of error messages - sigh

multiqc

extra program to install!

PATH issues within X2Go env shell.

in .bashrc change the PS1 line to this:
export PS1="[\033[38;5;220m]\u[\033[38;5;15m]@[\033[38;5;39m]$NICKNAME[\033[38;5;15m]:[\033[38;5;202m]\w[\033[38;5;15m]\$ "
in .bash_paths add the line below after PATH= and before $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:$HOME/bin:$HOME/.local/bin:

TrimGalore download path

Now hosted on github and file structure changed so this file - /genomics/software_tasks/trim_galore.yaml - needs to be updated to:

- name: Download Trim Galore! {{version}}
  get_url: url="https://github.com/FelixKrueger/TrimGalore/archive/{{version}}.zip" dest={{source_dir}}/trim_galore_v{{version}}.zip

- name: Unzip Trim Galore!
  unarchive:
    src: "{{source_dir}}/trim_galore_v{{version}}.zip"
    dest: "{{software_dir}}"
    copy: no
    creates: "{{software_dir}}/trim_galore_zip"

- name: Install Trim Galore!
  file: src="{{software_dir}}/TrimGalore-{{version}}/trim_galore" dest=/usr/local/bin/trim_galore state=link

qiime environment exists, script stops

if main software script fails post qiime environment install then the script won't complete as the environment already exists!

timezone

timezone isn't set to Czech/Europe...

no gedit

pluma is installed - same thing, symlink it.

pfamscan

missing perl libs!

get from here: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/PfamScan.tar.gz

and also install Moose

phylogenomics 1

ete3 won't compile Slr
python 3.4 is needed for ete, 3.5 is installed
jmodeltest not installed
trimal not installed
r8s

sudo mkdir /usr/include/sys
sudo cp --archive /usr/include/errno.h /usr/include/sys/errno.h
c'continuousML.h is missing from package

FastQC Failing

AMI - Beta 1

FastQC running but failing (both using GUI and CLI).

Error messages from CLI:

genomics@ip-10-142-246-2:~/workshop_materials/quality_control$ fastqc bartonella_illumina.fastq 
java.io.FileNotFoundException: /etc/fastqc/Configuration/adapter_list.txt (No such file or directory)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at java.io.FileInputStream.<init>(FileInputStream.java:93)
	at uk.ac.babraham.FastQC.Modules.AdapterContent.<init>(AdapterContent.java:75)
	at uk.ac.babraham.FastQC.Modules.ModuleFactory.getStandardModuleList(ModuleFactory.java:37)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:134)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:102)
	at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)
Started analysis of bartonella_illumina.fastq
java.io.FileNotFoundException: /etc/fastqc/Configuration/limits.txt (No such file or directory)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at java.io.FileInputStream.<init>(FileInputStream.java:93)
	at uk.ac.babraham.FastQC.Modules.ModuleConfig.readParams(ModuleConfig.java:87)
	at uk.ac.babraham.FastQC.Modules.ModuleConfig.<clinit>(ModuleConfig.java:35)
	at uk.ac.babraham.FastQC.Modules.PerTileQualityScores.processSequence(PerTileQualityScores.java:174)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:88)
	at java.lang.Thread.run(Thread.java:745)
Approx 5% complete for bartonella_illumina.fastq
Approx 15% complete for bartonella_illumina.fastq
Approx 30% complete for bartonella_illumina.fastq
Approx 40% complete for bartonella_illumina.fastq
Approx 50% complete for bartonella_illumina.fastq
Approx 60% complete for bartonella_illumina.fastq
Approx 70% complete for bartonella_illumina.fastq
Approx 80% complete for bartonella_illumina.fastq
Approx 90% complete for bartonella_illumina.fastq
Approx 100% complete for bartonella_illumina.fastq
Analysis complete for bartonella_illumina.fastq
Failed to process file bartonella_illumina.fastq
java.lang.IllegalArgumentException: No key called gc_sequence:ignore in the config data
	at uk.ac.babraham.FastQC.Modules.ModuleConfig.getParam(ModuleConfig.java:148)
	at uk.ac.babraham.FastQC.Modules.PerSequenceGCContent.ignoreInReport(PerSequenceGCContent.java:57)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:331)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:155)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110)
	at java.lang.Thread.run(Thread.java:745)
genomics@ip-10-142-246-2:~/workshop_materials/quality_control$

Fresh download of the FastQC zip file, unzip, making fastqc executable and symbolic link to /usr/bin fixed it:

wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip
cd FastQC 
chmod 755 fastqc 
sudo ln -s /home/master/FastQC/fastqc /usr/bin/