updated to python3 and debugged

.gitignore

@@ -5,6 +5,7 @@ pimmuno_2.py
 develop_data/
 venv/
 .cache/
+jobStore/
 test-report.xml
 __pycache__
 *.DONE

MANUAL.md

@@ -547,7 +547,7 @@ purposes:
     12: g/f/jobO4yiE4        return self.run(fileStore)
     13: g/f/jobO4yiE4      File "/home/ucsc/arjun/tools/dev/toil_clean/src/toil/job.py", line 1406, in run
     14: g/f/jobO4yiE4        rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs)
-    15: g/f/jobO4yiE4      File "/home/ucsc/arjun/tools/protect_toil_clean/local/lib/python2.7/site-packages/protect/binding_prediction/common.py", line 566, in merge_mhc_peptide_calls
+    15: g/f/jobO4yiE4      File "/home/ucsc/arjun/tools/protect_toil_clean/local/lib/python3/site-packages/protect/binding_prediction/common.py", line 566, in merge_mhc_peptide_calls
     16: g/f/jobO4yiE4        raise RuntimeError('No peptides available for ranking')
     17: g/f/jobO4yiE4    RuntimeError: No peptides available for ranking
     18: g/f/jobO4yiE4    ERROR:toil.worker:Exiting the worker because of a failed job on host sjcb10st7
@@ -581,9 +581,9 @@ do not store logs from tools (see BD2KGenomics/protect#275). The error looks sim
     Z/O/job1uH92D        return self.run(fileStore)
     Z/O/job1uH92D      File "/home/ucsc/arjun/tools/dev/toil_clean/src/toil/job.py", line 1406, in run
     Z/O/job1uH92D        rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs)
-    Z/O/job1uH92D      File "/home/ucsc/arjun/tools/protect_toil_clean/local/lib/python2.7/site-packages/protect/mutation_calling/radia.py", line 238, in run_filter_radia
+    Z/O/job1uH92D      File "/home/ucsc/arjun/tools/protect_toil_clean/local/lib/python3/site-packages/protect/mutation_calling/radia.py", line 238, in run_filter_radia
     Z/O/job1uH92D        tool_version=radia_options['version'])
-    Z/O/job1uH92D      File "/home/ucsc/arjun/tools/protect_toil_clean/local/lib/python2.7/site-packages/protect/common.py", line 138, in docker_call
+    Z/O/job1uH92D      File "/home/ucsc/arjun/tools/protect_toil_clean/local/lib/python3/site-packages/protect/common.py", line 138, in docker_call
     Z/O/job1uH92D        'for command \"%s\"' % ' '.join(call),)
     Z/O/job1uH92D    RuntimeError: docker command returned a non-zero exit status (1)for command "docker run --rm=true -v /scratch/bio/ucsc/toil-681c097c-61da-4687-b734-c5051f0aa19f/tmped2fnu/f041f939-5c0d-40be-a884-68635e929d09:/data --log-driver=none aarjunrao/filterradia:bcda721fc1f9c28d8b9224c2f95c440759cd3a03 TCGA-CH-5788 17 /data/radia.vcf /data /home/radia/scripts -d /data/radia_dbsnp -r /data/radia_retrogenes -p /data/radia_pseudogenes -c /data/radia_cosmic -t /data/radia_gencode --noSnpEff --noBlacklist --noTargets --noRnaBlacklist -f /data/hg38.fa --log=INFO -g /data/radia_filtered_chr17_radia.log"
     Z/O/job1uH92D    ERROR:toil.worker:Exiting the worker because of a failed job on host sjcb10st1

Makefile

@@ -45,17 +45,16 @@ help:
 	@echo "$$help"
 
 
-python=python2.7
-pip=pip2.7
+python=python
+pip=pip
 tests=src/protect/test/unit
 extras=
-
 green=\033[0;32m
 normal=\033[0m
 red=\033[0;31m
 
 prepare: check_venv
-	@$(pip) install toil==3.8.0 pytest==2.8.3
+	@$(pip) install toil pytest  
 
 develop: check_venv
 	$(pip) install -e .$(extras)
@@ -107,10 +106,10 @@ clean_pypi:
 
 clean: clean_develop clean_sdist clean_pypi
 
-
-check_venv:
-	@$(python) -c 'import sys; sys.exit( int( not hasattr(sys, "real_prefix") ) )' \
-		|| ( echo "$(red)A virtualenv must be active.$(normal)" ; false )
+#always fails, even though in a venv
+#check_venv:
+#	@$(python) -c 'import sys; sys.exit( int( not hasattr(sys, "real_prefix") ) )' \
+#		|| ( echo "$(red)A virtualenv must be active.$(normal)" ; false )
 
 
 check_clean_working_copy:

ProTECT_config.yaml

@@ -0,0 +1,169 @@
+## Copyright 2016 UCSC Computational Genomics Lab
+## Original contributor: Arjun Arkal Rao
+##
+## Licensed under the Apache License, Version 2.0 (the "License");
+## you may not use this file except in compliance with the License.
+## You may obtain a copy of the License at
+##
+##    http://www.apache.org/licenses/LICENSE-2.0
+##
+## Unless required by applicable law or agreed to in writing, software
+## distributed under the License is distributed on an "AS IS" BASIS,
+## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+## See the License for the specific language governing permissions and
+## limitations under the License.
+####################################################################################################
+####################################################################################################
+##  This is the input parameter file for the precision immuno pipeline.  The parameters for each of
+##  the tools is provided here.  The file is written in the YAML format.  A nice description of the
+##  format can be found at http://docs.ansible.com/ansible/YAMLSyntax.html
+##
+##  You can add comments anywhere in this file by prefixing it with a '#'
+##
+##  Unless otherwise mentioned, all fields must be filled.
+##
+####################################################################################################
+####################################################################################################
+
+# Any number of patients/samples can be listed here
+patients:
+    TEST:
+        tumor_dna_fastq_1: /home/drkthomp/gerald_D1VCPACXX_1.bam
+        normal_dna_fastq_2: /home/drkthomp/gerald_D1VCPACXX_6.bam
+        tumor_rna_fastq_2: /home/drkthomp//gerald_C1TD1ACXX_8_ACAGTG.bam
+        tumor_type: 'SKCM'
+
+# These are options that are used by most tools
+Universal_Options:
+    dockerhub: aarjunrao
+    java_Xmx: 12G
+    reference_build: hg38 # Acceptable options are hg38, hg38, GRCh37, GRCh38
+    # sse_key: /path/to/master.key # Path to the AWS master key.  Required if using AWS else optional
+    # sse_key_is_master: True # True or False.  Required if using AWS else optional
+    # gdc_download_token: /path/to/token.txt # Path to the user's GDC download token.
+    storage_location: Local # Local or aws:<bucket_name> for where the output must go
+    #storage_location: aws:protect-run-xyz
+    output_folder: /home/drkthomp/results # Path to where the output must go.
+    #mail_to: [email protected]  # Email patients:
+
+
+# for sending success report.
+
+
+# These options are for each module. You probably don't need to change any of this!
+alignment:
+    cutadapt:
+        a: AGATCGGAAGAG
+        A: AGATCGGAAGAG
+        # version: 1.9.1
+    star:
+        type: star # use starlong if your reads are > 150bp
+        index: /home/drkthomp/e/protect-data/star_with_fusion_100bp_readlen_indexes.tar.gz # Use star_without if you set star_fusion = False
+        # version: 2.5.2b
+    bwa:
+       index: /home/drkthomp/e/protect-data/bwa_index.tar.gz
+        # version: 0.7.9a
+    post:
+        samtools:
+            # version: 1.2
+        picard:
+            # version: 1.135
+
+expression_estimation:
+    rsem:
+        index: /home/drkthomp/e/protect-data/rsem_index.tar.gz
+        # version: 1.2.0
+
+mutation_calling:
+    indexes:
+        chromosomes: canonical_chr, chrM
+        genome_fasta: /home/drkthomp/e/protect-data/hg38.fa.tar.gz
+        genome_fai: /home/drkthomp/e/protect-data/hg38.fa.fai.tar.gz
+        genome_dict: /home/drkthomp/e/protect-data/hg38.dict.tar.gz
+        cosmic_vcf: /home/drkthomp/e/protect-data/CosmicCodingMuts.vcf.tar.gz
+        cosmic_idx: /home/drkthomp/e/protect-data/CosmicCodingMuts.vcf.idx.tar.gz
+        dbsnp_vcf: /home/drkthomp/e/protect-data/dbsnp_coding.vcf.gz
+        dbsnp_idx: /home/drkthomp/e/protect-data/dbsnp_coding.vcf.idx.tar.gz
+        dbsnp_tbi: /home/drkthomp/e/protect-data/dbsnp_coding.vcf.gz.tbi
+    mutect:
+        java_Xmx: 2G
+        # version: 1.1.7
+    muse:
+        # version: 1.0rc_submission_b391201
+    radia:
+        cosmic_beds: /home/drkthomp/e/protect-data/radia_cosmic.tar.gz
+        dbsnp_beds: /home/drkthomp/e/protect-data/radia_dbsnp.tar.gz
+        retrogene_beds: /home/drkthomp/e/protect-data/radia_retrogenes.tar.gz
+        pseudogene_beds: /home/drkthomp/e/protect-data/radia_pseudogenes.tar.gz
+        gencode_beds: /home/drkthomp/e/protect-data/radia_gencode.tar.gz
+        # version: 398366ef07b5911d8082ed61cbf03d487a41f286
+    somaticsniper:
+        # version: 1.0.4
+        samtools:
+            # version: 0.1.8
+        bam_readcount:
+            # version: 0.7.4
+    star_fusion:
+        #run: True
+        #version: 1.0.0
+    fusion_inspector:
+        #run_trinity: True
+        #version: 1.0.1
+    strelka:
+        # version: 1.0.15
+        config_file: /home/drkthomp/e/protect-data/strelka_bwa_WXS_config.ini.tar.gz
+
+
+mutation_annotation:
+    snpeff:
+        index: /home/drkthomp/e/protect-data/snpeff_index.tar.gz
+        # version: 3.6
+        java_Xmx: 20G
+
+mutation_translation:
+    transgene:
+        gencode_peptide_fasta : /home/drkthomp/e/protect-data/gencode.v25.pc_translations_NOPARY.fa.tar.gz
+        gencode_transcript_fasta : /home/drkthomp/e/protect-data/gencode.v25.pc_transcripts_NOPARY.fa.tar.gz
+        gencode_annotation_gtf : /home/drkthomp/e/protect-data/gencode.v25.annotation_NOPARY.gtf.tar.gz
+        genome_fasta : /home/drkthomp/e/protect-data/hg38.fa.tar.gz
+        # version: 2.2.2
+
+haplotyping:
+    phlat:
+        index: /home/drkthomp/e/protect-data/phlat_index.tar.gz
+        # version: 1.0
+
+mhc_peptide_binding:
+    mhci:
+        method_file: /home/drkthomp/e/protect-data/mhci_restrictions.json.tar.gz
+        pred: IEDB_recommended
+        # version: 2.13
+    mhcii:
+        method_file: /home/drkthomp/e/protect-data/mhcii_restrictions.json.tar.gz
+        pred: IEDB_recommended
+        # version: 2.13
+    netmhciipan:
+        # version: 3.1
+
+prediction_ranking:
+    rankboost:
+        mhci_args:
+            npa: 0.0
+            nph: 0.0
+            nMHC: 0.32
+            TPM: 0.0
+            overlap: 0.68
+            tndelta: 0.0
+        mhcii_args:
+            npa: 0.2
+            nph: 0.2
+            nMHC: 0.2
+            TPM: 0.2
+            tndelta: 0.2
+        # version: 2.0.3
+
+reports:
+    mhc_pathways_file: /home/drkthomp/e/protect-data/mhc_pathways.tsv.tar.gz
+    itx_resistance_file: /home/drkthomp/e/protect-data/itx_resistance.tsv.tar.gz
+    immune_resistance_pathways_file: /home/drkthomp/e/protect-data/immune_resistance_pathways.json.tar.gz
+    car_t_targets_file: /home/drkthomp/e/protect-data/car_t_targets.tsv.tar.gz

README.md

@@ -1,7 +1,10 @@
-[![Stories in Ready](https://badge.waffle.io/BD2KGenomics/protect.png?label=ready&title=Ready)](https://waffle.io/BD2KGenomics/protect)
 # ProTECT
 ### **Pr**ediction **o**f **T**-Cell **E**pitopes for **C**ancer **T**herapy
 
+Adapation of ProTECT to use python 3.8 instead of 2.7. Currently have tested a complete run using fastq files from [HCC1395 WGS Exome RNA Seq Data](https://github.com/genome/gms/wiki/HCC1395-WGS-Exome-RNA-Seq-Data), but have not checked results against the [original ProTECT](https://github.com/BD2KGenomics/protect) with TCGA PRAD yet. 
+
+Adaptation done using 2to3 and manual bug testing. Manual changes recorded [at changes.md](https://github.com/Dranion/protect/blob/master/changes.md). Since s3am is python2, **currently is local only**, however an untested python3 version of s3am exists [here](https://github.com/Dranion/bd2k-extras/tree/main). Continuing to the original README: 
+
 This repo contains the Python libraries for the Precision Immunology Pipeline developed at UCSC.
 
     src/protect/pipeline/ProTECT.py             - The python script for running the pipeline.