A few fixes

Dockerfile

@@ -5,7 +5,7 @@ FROM continuumio/miniconda3
 WORKDIR /app
 
 # Install supervisord
-RUN apt-get update && apt-get install -y supervisor
+RUN apt-get update && apt-get install -y supervisor default-jre-headless
 
 # Install slivka-bio using Conda
 RUN conda install anaconda-client -n base \
@@ -17,6 +17,9 @@ COPY ./settings.yml /opt/conda/envs/compbio-services/var/slivka-bio/
 # Copy supervisord config
 COPY supervisord.conf /etc/supervisor/conf.d/supervisord.conf
 
+# Mark services directory as extrernally mounted volume
+VOLUME /opt/conda/envs/compbio-services/var/slivka-bio/services
+
 # Expose the port Slivka is running on
 EXPOSE 8000
 

docker-compose.yml

@@ -4,6 +4,7 @@ services:
   slivka-bio:
     build: .
     volumes:
+      - ./services/:/opt/conda/envs/compbio-services/var/slivka-bio/services/:ro
       - media:/app/media
     ports:
       - "8080:8000"

services/aacon.service.yaml

@@ -0,0 +1,148 @@
+---
+slivka-version: 0.8.3
+name: AACon
+description: AACon is a set of tools implementing 17 different conservation
+  scores reviewed by Valdar as well as the more complex SMERFS algorithm
+  for predicting protein functional sites.
+author: "Agnieszka Golicz, Peter V. Troshin, F\xE1bio Madeira"
+version: '1.1'
+license: Apache 2.0
+
+classifiers:
+- 'Topic :: Computational biology :: Sequence analysis'
+- 'Operation :: Analysis :: Sequence analysis :: Sequence alignment analysis
+  :: Sequence alignment analysis (conservation)'
+- 'Operation :: Analysis :: Sequence analysis :: Protein sequence analysis'
+
+parameters:
+  input:
+    name: Input file
+    type: file
+    required: true
+    media-type: application/fasta
+
+  normalize:
+    name: Normalize
+    description: Normalize the results. Normalized results have values between
+      0 and 1. Please note however, that some results cannot be normalized.
+      In such a case, the system returns not normalized value. The following
+      formula is used for normalization n = (d - dmin)/(dmax - dmin). Negative
+      results first converted to positive by adding a greatest absolute
+      result value.
+    type: boolean
+    required: false
+    default: false
+
+  method:
+    name: Calculation method
+    description: The method of the calculation to use
+    type: choice[]
+    required: false
+    default: [shenkin]
+    choices:
+      kabat: KABAT
+      jores: JORES
+      schneider: SCHNEIDER
+      shenkin: SHENKIN
+      gerstein: GERSTEIN
+      taylor gaps: TAYLOR_GAPS
+      taylor no gaps: TAYLOR_NO_GAPS
+      zvelibil: ZVELIBIL
+      karlin: KARLIN
+      armon: ARMON
+      thompson: THOMPSON
+      not lancet: NOT_LANCET
+      mirny: MIRNY
+      williamson: WILLIAMSON
+      landgraf: LANDGRAF
+      sander: SANDER
+      valdar: VALDAR
+      smerfs: SMERFS
+
+  smerfsww:
+    name: SMERFS Window Width
+    description: The width of the window for SMERFS. Optional, defaults to 7
+    type: int
+    required: false
+    min: 3
+    max: 100
+    default: 7
+
+  smerfscs:
+    name: SMERFS Column Scoring Method
+    description: 'SMERFS Column Score algorithm defines the window scores
+      to columns allocation, two methods are possible: MID_SCORE - gives
+      the window score to the middle column, MAX_SCORE - gives the column
+      the highest score of all the windows it belongs to. Optional defaults
+      to MID_SCORE.'
+    type: choice
+    required: false
+    choices:
+      max score: MAX_SCORE
+      mid score: MID_SCORE
+    default: mid score
+
+  smerfsgt:
+    name: SMERFS Gap Threshhold
+    description: a gap percentage cutoff - a float greater than 0 and smaller
+      or equal 1.  Optional defaults to 0.1
+    type: float
+    required: false
+    min: 0.001
+    max: 1
+    default: 0.1
+
+command:
+- bash
+- ${SLIVKA_HOME}/bin/AACon.sh
+
+args:
+  input:
+    arg: -i=$(value)
+    symlink: data.align
+  normalize:
+    arg: -n
+  method:
+    arg: -m=$(value)
+    join: ','
+  smerfsww:
+    arg: -smerfsWW=$(value)
+  smerfscs:
+    arg: -smerfsCS=$(value)
+  smerfsgt:
+    arg: -smerfsGT=$(value)
+  _const0:
+    arg: -d=stat.txt
+    default: present
+  _const1:
+    arg: -f=RESULT_NO_ALIGNMENT
+    default: present
+  _const2:
+    arg: -o=output.txt
+    default: present
+
+outputs:
+  raw-output:
+    path: output.txt
+    media-type: text/plain
+  jalview-annotations:
+    path: aacon.jvannot
+    media-type: application/jalview-annotations
+  log:
+    path: stat.txt
+    media-type: text/plain
+  error-log:
+    path: stderr
+    media-type: text/plain
+
+execution:
+  runners:
+    default:
+      type: SlivkaQueueRunner
+
+tests:
+- applicable-runners: ["default"]
+  parameters:
+    input: ${SLIVKA_HOME}/testdata/uniref50.fa
+  timeout: 5
+...

services/clustalo.service.yaml

@@ -0,0 +1,133 @@
+---
+slivka-version: 0.8.3
+name: ClustalO
+description: Clustal Omega is the latest addition to the Clustal family.
+  It offers a significant increase in scalability over previous versions,
+  allowing hundreds of thousands of sequences to be aligned in only 
+  a few hours. It will also make use of multiple processors, where present. 
+  In addition, the quality of alignments is superior to previous versions, 
+  as measured by a range of popular benchmarks. 
+author: Fabian Sievers, Andreas Wilm, David Dineen, Johannes Söding,
+  Michael Remmert
+version: '1.2.4'
+license: GNU GPL ver. 2
+
+classifiers:
+- 'Topic :: Computational biology :: Sequence analysis'
+- 'Operation :: Analysis :: Sequence analysis :: Sequence alignment :: Multiple
+  sequence alignment'
+
+parameters:
+  input:
+    name: Input file
+    type: file
+    required: true
+#    max-size: 4MB
+    media-type: application/fasta
+
+  dealign:
+    name: Dealign
+    description: Dealign input sequences
+    type: boolean
+    default: false
+    required: false
+
+  full-distance:
+    name: Full distance matrix
+    description: Use full distance matrix for guide-tree calculation (slow;
+      mBed is default)
+    type: boolean
+    default: false
+    required: false
+
+  full-distance-iteration:
+    name: Full distance matrix for each iteration
+    description: Use full distance matrix for guide-tree calculation during
+      iteration (mBed is default)
+    type: boolean
+    default: false
+    required: false
+
+  max-hmm-iterations:
+    name: Max Guide tree iterations
+    description: Maximum number of HMM iterations
+    type: int
+    min: 1
+    max: 100
+    default: 1
+
+  iterations:
+    name: Number of iterations (combined)
+    description: Number of (combined guide tree/HMM) iterations
+    type: int
+    min: 1
+    max: 100
+    default: 1
+
+  max-guidetree-iterations:
+    name: Max Guide tree iterations
+    description: Maximum guide tree iterations
+    type: int
+    min: 1
+    max: 100
+    default: 1
+
+command:
+- clustalo
+
+args:
+  input:
+    arg: --infile=$(value)
+    symlink: input.txt
+  dealign:
+    arg: --dealign
+  full-distance:
+    arg: --full
+  full-distance-iteration:
+    arg: --full-iter
+  max-hmm-iterations:
+    arg: --max-hmm-iterations=$(value)
+  iterations:
+    arg: --iter=$(value)
+  max-guidetree-iterations:
+    arg: --max-guidetree-iterations=$(value)
+  _const0:
+    arg: --outfile=output.txt
+    default: present
+  _const1:
+    arg: --outfmt=clustal
+    default: present
+  _const2:
+    arg: -v
+    default: present
+  _const3:
+    arg: --log=stat.log
+    default: present
+  _const4:
+    arg: --threads=1
+    default: present
+
+outputs:
+  alignment:
+    path: output.txt
+    media-type: application/clustal
+  tree:
+    path: input.dnd
+  log:
+    path: stat.log
+    media-type: text/plain
+  error-log:
+    path: stderr
+    media-type: text/plain
+
+execution:
+  runners:
+    default:
+      type: SlivkaQueueRunner
+
+tests:
+- applicable-runners: ["default"]
+  parameters:
+    input: ${SLIVKA_HOME}/testdata/uniref50.fa
+  timeout: 5
+...