Problems with dockers

[mult1fractal]

General thread to talk and solve Dockerfile issues

[mult1fractal]

PhySpy

Hab den Docker für PhySpi fertig:

FROM continuumio/miniconda2
RUN apt-get update && apt install -y procps git wget make gcc g++ unzip && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN conda config --add channels conda-forge && \
    conda config --add channels bioconda && \
    conda config --add channels default


# Package randomForest in R - version 4.5-36 or later
RUN     conda install -c conda-forge r-randomforest && \
        conda install -c conda-forge/label/gcc7 r-randomforest && \
        conda install -c conda-forge/label/cf201901 r-randomforest && \
        conda install -c scikit-learn


#get git
RUN git clone https://github.com/linsalrob/PhiSpy.git
RUN cd /PhiSpy && \
       make

RUN cd /PhiSpy && \
    chmod a+x * 

ENV PATH /PhiSpy:$PATH

• build funktioniert
• example input funktioniert auch
  Inhalt vom test inputdir:

(base) root@3629ca1b762e:/PhiSpy/Test_Organism/160490.1# ls Features TAXONOMY annotations contigs GENOME TAXONOMY_ID assigned_functions

• allerdings laufen unsere nicht unsere Testdaten -.-

(base) root@f7b9fccd7393:/# PhiSpy.py -i /home/mike/Documents/De-Phage/local_Docker_dev/testfolder/all_drafts/OX2_draft.fa -o outputdir -t 25 Cannot open /home/mike/Documents/De-Phage/local_Docker_dev/testfolder/all_drafts/OX2_draft.fa/contigs

• funktioniert nicht
• /foobar/OX2_Draft.fa existiert aber die msg zeigt das da noch /contigs irgenwo sein soll... gibts aber nicht

---

• muss wahrscheinlich unsere .fa vorher noch mit SEED /RAST annotieren

% ./PhiSpy.py -i organism_directory -o output_directory -c

where: 'output directory': Output directory is the directory where the final output file will be created.

'organism directory': The seed annotation directory for the input bacterial organism whose prophage(s) need to be identified.

You can download the SEED genomes from the PhAnToMe database

Or, If you have new genome, you can annotate it using the RAST server. After annotation, you can download the genome directory from the server.

Or, If you have the GenBank file (containing sequence) of the genome, you can convert it using the following command: % python genbank_to_seed.py GenBank_file.gb organism_directory

Now to run PhiSpy, use organism_directory as 'organism directory'.

[replikation]

die anwendung sieht complexer aus mit diesen seed genomen:
http://www.phantome.org/Downloads/genomes/seed/
naja adde das dockerfile und bau den auf docker hub.

Versuche mal rauszubekommen was du alles machen muss um das analysieren. genbank files kann man mit prokka erstellen. das kann ich einbauen.

[mult1fractal]

Phigaro

• Problem:
  • Please, create config file using phigaro-setup script
  • das setup fragt den Pfad zu hmmer und prodigal und einer db aktualisierung ab
  • wir wollten das über printf "1\n1\nn" && phigaro-setup --no-updatedb lösen
  • im /bin/bash docker funktioniert das, aber nicht wenn die Dockerfile baut

From continuumio/miniconda3
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt install -y procps git locate wget make gcc && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN conda config --add channels conda-forge && \
    conda config --add channels bioconda && \
    conda config --add channels default


####Dockerfile
Run conda install hmmer prodigal

#get git
Run git clone https://github.com/bobeobibo/phigaro.git


#install Phigaro
#     printf "1\n1\nn" | phi.....  beantwortet alle fragen
RUN cd phigaro && \
    pip install phigaro && \
    chmod a+x * && \
    printf "1\n1\nn" | phigaro-setup --no-updatedb
  #  phigaro-setup --no-updatedb 


# datenbank download dauert 30 min 

ENV PATH /Phigaro:$PATH

# 
# phigaro -f /phigaro/test_data/Bacillus_anthracis_str_ames.fna -e txt html stdout -o result
#ergebnisdatei ist result

build und Error-msg

Please select appropriate Prodigal location
[1] /opt/conda/bin/prodigal
[2] Add another path manually
Choose your option (Enter for /opt/conda/bin/prodigal): Please select appropriate HMMER location
[1] /opt/conda/bin/hmmsearch
[2] Add another path manually
Choose your option (Enter for /opt/conda/bin/hmmsearch):

• dann hängt es ne Ewigkeit und nichts passiert

[mult1fractal]

Meine Idee zu Phigaro:

• das git zu forken und den phigaro setup Befehl suchen und die querys löschen

[replikation]

@Stormrider935

• for something like this attach an echo "1" to it. you did this already. its waiting for a user input

Please select appropriate Prodigal location
[1] /opt/conda/bin/prodigal
[2] Add another path manually
Choose your option (Enter for /opt/conda/bin/prodigal): Please select appropriate HMMER location
[1] /opt/conda/bin/hmmsearch
[2] Add another path manually
Choose your option (Enter for /opt/conda/bin/hmmsearch):

[mult1fractal]

• i have the same problem if i attach another 1 to the code like this printf '1\n1\n1\nn'
• it still stops here ..

Please select appropriate Prodigal location
[1] /opt/conda/bin/prodigal
[2] Add another path manually
Choose your option (Enter for /opt/conda/bin/prodigal): Please select appropriate HMMER location
[1] /opt/conda/bin/hmmsearch
[2] Add another path manually
Choose your option (Enter for /opt/conda/bin/hmmsearch):

[mult1fractal]

• Problem solved.. maybe...

• I tried the following base image: From continuumio/miniconda2 and not miniconda 3

• build process seems to work | sitll downloading database

• but it's python 2.7....

• works finally with the provided Testdata... only in /Phigaro folder

• Path is not the Problem

• WORKDIR is /Phigaro, but not sure how nextflow will handle it

[replikation]

we cant go into the /phigaro workdir. we have a separate process dir in nextflow

[mult1fractal]

• phigaro takes only ctgs > 20000bp
• smaller ctgs will not be analyzed
• for module:

"""
printf 'Y' | phigaro -f test_data/Bacillus_anthracis_str_ames.fna -o test_data/Bacillus_anthracis_str_ames.phg -p --not-open -c /phigaro/config.yml
"""

• parse Y because phigaro asks if it should start w/o smaller ctgs