guyleonard / evomics_2017 Goto Github PK
View Code? Open in Web Editor NEWCreating the AMI for the evomics.org Workshops
Creating the AMI for the evomics.org Workshops
gatb - either not installed or not in /usr/bin
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...
it's in software but not in path..also needs a download/install task...
If qiime 1 env installs are already installed the playbook will fail at trying to reinstall
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.
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 is hardcoded in evomics_2017/genomics/software_tasks/samtools.yaml
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 install makes dandling links to github dir rather than the software dir...
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.
loads of error messages - sigh
extra program to install!
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:$HOME/.local/bin:
Now hosted on github and file structure changed so this file - /genomics/software_tasks/trim_galore.yaml - needs to be updated to:
- name: Download Trim Galore! {{version}}
get_url: url="https://github.com/FelixKrueger/TrimGalore/archive/{{version}}.zip" dest={{source_dir}}/trim_galore_v{{version}}.zip
- name: Unzip Trim Galore!
unarchive:
src: "{{source_dir}}/trim_galore_v{{version}}.zip"
dest: "{{software_dir}}"
copy: no
creates: "{{software_dir}}/trim_galore_zip"
- name: Install Trim Galore!
file: src="{{software_dir}}/TrimGalore-{{version}}/trim_galore" dest=/usr/local/bin/trim_galore state=link
if main software script fails post qiime environment install then the script won't complete as the environment already exists!
timezone isn't set to Czech/Europe...
pluma is installed - same thing, symlink it.
missing perl libs!
get from here: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/PfamScan.tar.gz
and also install Moose
ete3 won't compile Slr
python 3.4 is needed for ete, 3.5 is installed
jmodeltest not installed
trimal not installed
r8s
AMI - Beta 1
FastQC running but failing (both using GUI and CLI).
Error messages from CLI:
genomics@ip-10-142-246-2:~/workshop_materials/quality_control$ 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/
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