fragpipe fails templating config file

[mvdbeek]

From https://sentry.galaxyproject.org/share/issue/da466f63ec5541e58db2ce827ada3918/. I can't see any use of $protein in the configfile, but this is not easy to read. These were the selection options for that job:

 482903706 | 60429780 | license_agreements | true
 482903707 | 60429780 | inputs             | {"values": [{"id": 135029103, "src": "hda"}, {"id": 135029113, "src": "hda"}, {"id": 135029181, "src": "hda"}, {"id": 135029899, "src": "hda"}, {"id": 135029941, "src": "hda"}, {"id": 135029997, "src": "hda"}, {"id": 1
35030021, "src": "hda"}, {"id": 135030047, "src": "hda"}, {"id": 135030099, "src": "hda"}, {"id": 135030110, "src": "hda"}, {"id": 135030123, "src": "hda"}, {"id": 135030143, "src": "hda"}, {"id": 135030187, "src": "hda"}, {"id": 135030202, "src": "hda"}, {"id":
135030223, "src": "hda"}, {"id": 135030366, "src": "hda"}, {"id": 135030419, "src": "hda"}, {"id": 135030441, "src": "hda"}, {"id": 135030478, "src": "hda"}, {"id": 135031201, "src": "hda"}, {"id": 135031209, "src": "hda"}, {"id": 135031217, "src": "hda"}, {"id":
 135031226, "src": "hda"}, {"id": 135031237, "src": "hda"}, {"id": 135031252, "src": "hda"}, {"id": 135031272, "src": "hda"}, {"id": 135031323, "src": "hda"}, {"id": 135031472, "src": "hda"}, {"id": 135031512, "src": "hda"}, {"id": 135031535, "src": "hda"}, {"id"
: 135031688, "src": "hda"}, {"id": 135031700, "src": "hda"}, {"id": 135031723, "src": "hda"}, {"id": 135032290, "src": "hda"}, {"id": 135032928, "src": "hda"}, {"id": 135032964, "src": "hda"}]}
 482903708 | 60429780 | input_prefix       | "V1"
 482903709 | 60429780 | manifest           | {"values": [{"id": 135038097, "src": "hda"}]}
 482903710 | 60429780 | database_name      | {"values": [{"id": 135036982, "src": "hda"}]}
 482903711 | 60429780 | database_options   | "decoy_and_contam"
 482903712 | 60429780 | num_slices         | "1"
 482903713 | 60429780 | wf                 | {"__current_case__": 0, "msfragger": {"advanced_options": {"group_variable": null, "output_format": "pepXML_pin", "output_max_expect": "50.0", "output_report_topN": "1", "report_alternative_proteins": true, "write_cali
brated_mzml": false, "write_uncalibrated_mgf": false}, "digestion": {"allowed_missed_cleavage": "2", "digest": {"__current_case__": 11, "search_enzyme": "nonspecific", "search_enzyme_cut": "-", "search_enzyme_name": "nonspecific", "search_enzyme_nocut": ""}, "dig
est_mass_range_max": "5000.0", "digest_mass_range_min": "500.0", "digest_max_length": "100", "digest_min_length": "7", "enzyme2": {"__current_case__": 0, "digest2": "no"}, "num_enzyme_termini": "2", "search_enzyme_sense": "C"}, "glyco_labile": {"Y_type_masses": "
", "diagnostic_fragments": "", "diagnostic_intensity_filter": "0.0", "labile_search_mode": "off", "min_sequence_matches": "2", "remainder_fragment_masses": null}, "mass_offsets": {"mass_offsets": "0", "restrict_deltamass_to": "all"}, "modeling_output": {"deisotop
e": null, "deneutralloss": true, "fragment_ion_series": null, "max_fragment_charge": "", "min_fragments_modelling": "", "min_matched_fragments": ""}, "open_search": {"add_topN_complementary": "", "delta_mass_exclude_ranges_max": "3.5", "delta_mass_exclude_ranges_
min": "-1.5", "localize_delta_mass": false, "mass_diff_to_variable_mod": "0", "track_zero_topN": "", "zero_bin_accept_expect": "", "zero_bin_mult_expect": ""}, "search_tolerances": {"calibrate_mass": "2", "fragment": {"__current_case__": 1, "fragment_mass_toleran
ce": "20", "fragment_mass_units": "ppm"}, "isotope_error": "0/1", "precursor": {"__current_case__": 1, "precursor_mass_lower": "-50", "precursor_mass_units": "ppm", "precursor_mass_upper": "50"}, "precursor_true": {"__current_case__": 0, "precursor_true_units": "
default"}}, "spectrum_processing": {"activation_types": "all", "check_spectral_files": true, "clear": {"clear_mz_range_max": "0.0", "clear_mz_range_min": "0.0"}, "intensity_transform": "0", "minimum_peaks": "", "minimum_ratio": "", "precursor": {"__current_case__
": 0, "override_charge": "default"}, "precursor_mass_mode": null, "remove_precursor_peak": "1", "remove_precursor_range_max": "1.5", "remove_precursor_range_min": "-1.5", "require_precursor": true, "reuse_dia_fragment_peaks": false, "use_topN_peaks": ""}, "static
_modification": {"add_A_alanine": "", "add_B_user_amino_acid": "", "add_C_cysteine": "57.021", "add_Cterm_peptide": "", "add_Cterm_protein": "", "add_D_aspartic_acid": "", "add_E_glutamic_acid": "", "add_F_phenylalanine": "", "add_G_glycine": "", "add_H_histidine
": "", "add_I_isoleucine": "", "add_J_user_amino_acid": "", "add_K_lysine": "", "add_L_leucine": "", "add_M_methionine": "", "add_N_asparagine": "", "add_Nterm_peptide": "", "add_Nterm_protein": "", "add_O_user_amino_acid": "", "add_P_proline": "", "add_Q_glutami
ne": "", "add_R_arginine": "", "add_S_serine": "", "add_T_threonine": "", "add_U_user_amino_acid": "", "add_V_valine": "", "add_W_tryptophan": "", "add_X_user_amino_acid": "", "add_Y_tyrosine": "", "add_Z_user_amino_acid": ""}, "variable_modification": {"allow_mu
ltiple_variable_mods_on_residue": null, "clip_nTerm_M": null, "max_variable_mods_combinations": "5000", "max_variable_mods_per_peptide": "3", "use_all_mods_in_first_search": null, "variable_mods": "43.006,KR,3;0.984,NQ,3", "variable_mods_select": ["15.99491461956
 M 3", "42.0105646837 [^ 1"]}}, "ptms": {"ptm_shepherd": {"__current_case__": 1, "run_ptm_shepherd": "no"}}, "quant_iso": {"isobaric_quantification": {"__current_case__": 1, "isobaric_quantification_step": "no"}}, "quant_ms1": {"label_free_quantification": {"__cu
rrent_case__": 2, "ionquant": {"advanced": {"excludemods": null, "locprob": "", "minisotopes": "", "minscans": "", "writeindex": null}, "feature_detection": {"imtol": "", "mztol": "", "rttol": ""}, "labeling_conditional": {"__current_case__": 0, "labeling_option"
: "lfq", "lfq": {"maxlfq": null, "minions": ""}}, "mbr": {"ionfdr": "", "mbrimtol": "", "mbrmincorr": "", "mbrrttol": "", "mbrtoprun": "", "peptidefdr": "", "proteinfdr": ""}, "normalization": "0", "topn": {"minexps": "", "minfreq": "", "tp": ""}}, "label_free_qu
antification_run": "ionquant"}}, "validation": {"validation_tab": {"__current_case__": 0, "phi_report": {"__current_case__": 0, "phi_report_opts": {"dont_use_prot_prophet_file": false, "print_decoys": false}, "run_phi_report": "true"}, "protein_prophet": {"__curr
ent_case__": 1, "run_protein_prophet": "false"}, "psm_validation": {"__current_case__": 1, "percolator": {"keep_tsv_files": false, "min_prob": "0.5"}, "run_psm_validation": "percolator"}, "run_validation": "true"}}, "workflow_name": "Default"}
 482903714 | 60429780 | workflow_only      | false
 482903715 | 60429780 | output_options     | ["workflow", "log", "combined_outputs", "concatenated_outputs"]
 482903716 | 60429780 | chromInfo          | "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
 482903717 | 60429780 | dbkey              | "?"
 482903718 | 60429780 | __input_ext        | "input"

[bgruening]

I hope that one has fixed it https://github.com/galaxyproteomics/tools-galaxyp/pull/774

@reid-wagner can you confirm?

[mvdbeek]

I don't understand where we're accessing the protein variable, but I can update and try.

[reid-wagner]

Yeah - it's not obvious to me what the issue is, because there's no plain $protein variable as @mvdbeek said. I'll dig into it. Thanks for bringing this to attention.