# HG changeset patch # User galaxyp # Date 1368223102 14400 # Node ID 0578e296cab45cff7d55e2f3efbf144a82ac0579 Initial commit. diff -r 000000000000 -r 0578e296cab4 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Fri May 10 17:58:22 2013 -0400 @@ -0,0 +1,11 @@ +--2012-09-19 08:46:18-- http://www.apache.org/licenses/LICENSE-2.0.txt +Resolving www.apache.org... 140.211.11.131, 192.87.106.229, 2001:610:1:80bc:192:87:106:229 +Connecting to www.apache.org|140.211.11.131|:80... connected. +HTTP request sent, awaiting response... 200 OK +Length: 11358 (11K) [text/plain] +Saving to: “LICENSE-2.0.txt” + + 0K .......... . 100% 200K=0.06s + +2012-09-19 08:46:18 (200 KB/s) - “LICENSE-2.0.txt” saved [11358/11358] + diff -r 000000000000 -r 0578e296cab4 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri May 10 17:58:22 2013 -0400 @@ -0,0 +1,40 @@ +Tool wrapper for SearchGUI + PeptideShaker. This tool takes any number +of mgf files and performs X! Tandem and OMSSA searches on these via +SearchGUI and merges the results using PeptideShaker. + +For Galaxy-P we are installing this tool via CloudBioLinux +(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While +this fabric script may not be exactly appropriate for your environment +it may serve as a template for how to install this software. In +particular these tools require CLI wrappers to be placed for +PeptideShaker and SearchGUI that can be installed as demostrated in +these fabric functions. + +Note: Also SearchGUI requires a version greater than 1.12.2 which +contained several bugs preventing this from working on the +command-line and via Linux. + +Also, PeptideShaker may require xvfb to simulate an X environment if +this is installed on a headless server. +# Obtaining Tools + +Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/. + +# Contact + +Please send suggestions for improvements and bug reports to +jmchilton@gmail.com. + +# License + +All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented. + +# Tool Versioning + +Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta. diff -r 000000000000 -r 0578e296cab4 README_GALAXYP.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_GALAXYP.md Fri May 10 17:58:22 2013 -0400 @@ -0,0 +1,22 @@ +# Obtaining Tools + +Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/. + +# Contact + +Please send suggestions for improvements and bug reports to +jmchilton@gmail.com. + +# License + +All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented. + +# Tool Versioning + +Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta. diff -r 000000000000 -r 0578e296cab4 README_REPO.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_REPO.md Fri May 10 17:58:22 2013 -0400 @@ -0,0 +1,18 @@ +Tool wrapper for SearchGUI + PeptideShaker. This tool takes any number +of mgf files and performs X! Tandem and OMSSA searches on these via +SearchGUI and merges the results using PeptideShaker. + +For Galaxy-P we are installing this tool via CloudBioLinux +(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While +this fabric script may not be exactly appropriate for your environment +it may serve as a template for how to install this software. In +particular these tools require CLI wrappers to be placed for +PeptideShaker and SearchGUI that can be installed as demostrated in +these fabric functions. + +Note: Also SearchGUI requires a version greater than 1.12.2 which +contained several bugs preventing this from working on the +command-line and via Linux. + +Also, PeptideShaker may require xvfb to simulate an X environment if +this is installed on a headless server. diff -r 000000000000 -r 0578e296cab4 build_mods_loc.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build_mods_loc.py Fri May 10 17:58:22 2013 -0400 @@ -0,0 +1,12 @@ +#!/usr/bin/env python + +import xml.etree.ElementTree as ET +from os.path import exists + +with open("searchgui_mods.loc", "w") as output: + for mods_path in ["searchGUI_mods.xml", "searchGUI_usermods.xml"]: + tree = ET.parse(mods_path) + modifications_el = tree.getroot() + for mod in modifications_el.findall("{http://www.ncbi.nlm.nih.gov}MSModSpec"): + name_el = mod.find("{http://www.ncbi.nlm.nih.gov}MSModSpec_name") + output.write("%s\n" % name_el.text.lower()) diff -r 000000000000 -r 0578e296cab4 peptide_shaker.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peptide_shaker.xml Fri May 10 17:58:22 2013 -0400 @@ -0,0 +1,221 @@ + + + + Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. + + + mkdir spectra; + mkdir output; + mkdir output_reports; + cwd=`pwd`; + #for $mgf in $peak_lists: + #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" + ln -s '$mgf' 'spectra/$input_name'; + #end for + SearchCLI \ + -spectrum_files \$cwd/spectra \ + -output_folder \$cwd/output \ + -ppm $precursor_ion_tol_units \ + -prec_tol $precursor_ion_tol \ + -frag_tol $fragment_tol \ + -enzyme '$enzyme' \ + #set $fixed_mods_str = $fixed_modifications or '' + #set $variable_mods_str = $variable_modifications or '' + #if $fixed_mods_str + -fixed_mods "$fixed_mods_str" \ + #end if + #if $variable_mods_str + -variable_mods "$variable_mods_str" \ + #end if + -mc $missed_cleavages \ + #if $advanced.specify: + -xtandem $advanced.xtandem \ + #if $advanced.omssa.run_omssa + #set $omssa = 1 + #else + #set $omssa = 0 + #end if + -omssa $omssa \ + #if $omssa == 1 + -hitlist_length ${advanced.omssa.hitlist_length} \ + -remove_prec ${advanced.omssa.remove_precursor} \ + -scale_prec ${advanced.omssa.scale_precursor} \ + -estimate_charge ${advanced.omssa.estimate_charge} \ + #end if + #end if + -db $input_database; + PeptideShakerCLI \ + -experiment 'Galaxy Experiment' \ + -sample 'Sample' \ + -replicate 1 \ + -spectrum_files \$cwd/spectra \ + -identification_files \$cwd/output \ + -search_params \$cwd/output/SearchGUI.parameters \ + -out_txt_1 \$cwd/output_reports \ + #if $processing_options.specify + -protein_FDR ${processing_options.protein_fdr} \ + -peptide_FDR ${processing_options.peptide_fdr} \ + -psm_FDR ${processing_options.psm_fdr} \ + -psm_FLR ${processing_options.psm_flr} \ + #if str($processing_options.a_score.use) == "1" + #set $a_score = 1 + #else + #set $a_score = 0 + #end if + -a_score $a_score \ + #if str($a_score) == "1" + -a_score_neutral_losses ${processing_options.a_score.neutral_losses} \ + #end if + #end if + #if $filtering_options.specify + -min_peptide_length ${filtering_options.min_peptide_length} \ + -max_peptide_length ${filtering_options.max_peptide_length} \ + -max_precursor_error ${filtering_options.max_precursor_error} \ + -max_precursor_error_type ${filtering_options.max_precursor_error_type} \ + -max_xtandem_e ${filtering_options.max_xtandem_e} \ + -max_omssa_e ${filtering_options.max_omssa_e} \ + -exclude_unknown_ptms ${filtering_options.exclude_unknown_ptms} \ + #end if + -out \$cwd/output.cps ; + mv output_reports/*peptides.txt peptides.txt ; + mv output_reports/*psms.txt psms.txt ; + mv output_reports/*proteins.txt proteins.txt + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + peptide_shaker + searchgui + + +**What it does** + +------ + +**Citation** + +For the underlying tool, please cite `TODO` + +If you use this tool in Galaxy, please cite TODO + + diff -r 000000000000 -r 0578e296cab4 searchGUI_mods.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchGUI_mods.xml Fri May 10 17:58:22 2013 -0400 @@ -0,0 +1,3021 @@ + + + + + 0 + + + 0 + + methylation of K + 14.015650 + 14.0266 + 0 + + K + + 34 + Methyl + + + + 1 + + + 0 + + oxidation of M + 15.994915 + 15.9994 + 0 + + M + + 35 + Oxidation + + + + 2 + + + 0 + + carboxymethyl C + 58.005479 + 58.0361 + 0 + + C + + 6 + Carboxymethyl + + + + 3 + + + 0 + + carbamidomethyl C + 57.021464 + 57.0513 + 0 + + C + + 4 + Carbamidomethyl + + + + 4 + + + 0 + + deamidation of N and Q + 0.984016 + 0.9848 + 0 + + N + Q + + 7 + Deamidated + + + + 5 + + + 0 + + propionamide C + 71.037114 + 71.0779 + 0 + + C + + 24 + Propionamide + + + + 6 + + + 0 + + phosphorylation of S + 79.966331 + 79.9799 + 0 + + S + + 21 + Phospho + + + + 7 + + + 0 + + phosphorylation of T + 79.966331 + 79.9799 + 0 + + T + + 21 + Phospho + + + + 8 + + + 0 + + phosphorylation of Y + 79.966331 + 79.9799 + 0 + + Y + + 21 + Phospho + + + + 9 + + + 2 + + M cleavage from protein n-term + -131.040485 + -131.1961 + 0 + + M + + 765 + Met-loss + + + + 10 + + + 1 + + acetylation of protein n-term + 42.010565 + 42.0367 + 0 + 1 + Acetyl + + + + 11 + + + 1 + + methylation of protein n-term + 14.015650 + 14.0266 + 0 + 34 + Methyl + + + + 12 + + + 1 + + tri-methylation of protein n-term + 42.046950 + 42.0797 + 0 + 37 + Trimethyl + + + + 13 + + + 0 + + beta methythiolation of D + 45.987721 + 46.0916 + 0 + + D + + 39 + Methylthio + + + + 14 + + + 0 + + methylation of Q + 14.015650 + 14.0266 + 0 + + Q + + 34 + Methyl + + + + 15 + + + 0 + + tri-methylation of K + 42.046950 + 42.0797 + 0 + + K + + 37 + Trimethyl + + + + 16 + + + 0 + + methylation of D + 14.015650 + 14.0266 + 0 + + D + + 34 + Methyl + + + + 17 + + + 0 + + methylation of E + 14.015650 + 14.0266 + 0 + + E + + 34 + Methyl + + + + 18 + + + 7 + + methylation of peptide c-term + 14.015650 + 14.0266 + 0 + 34 + Methyl + + + + 19 + + + 0 + + tri-deuteromethylation of D + 17.034480 + 17.0451 + 0 + + D + + 298 + Methyl:2H(3) + + + + 20 + + + 0 + + tri-deuteromethylation of E + 17.034480 + 17.0451 + 0 + + E + + 298 + Methyl:2H(3) + + + + 21 + + + 7 + + tri-deuteromethylation of peptide c-term + 17.034480 + 17.0451 + 0 + 298 + Methyl:2H(3) + + + + 22 + + + 1 + + n-formyl met addition + 159.035399 + 159.2062 + 0 + 107 + FormylMet + + + + 23 + + + 0 + + 2-amino-3-oxo-butanoic acid T + -2.015650 + -2.0159 + 0 + + T + + 401 + Didehydro + + + + 24 + + + 0 + + acetylation of K + 42.010565 + 42.0367 + 0 + + K + + 1 + Acetyl + + + + 25 + + + 7 + + amidation of peptide c-term + -0.984016 + -0.9848 + 0 + 2 + Amidated + + + + 26 + + + 0 + + beta-methylthiolation of D (duplicate of 13) + 45.987721 + 46.0916 + 0 + + D + + 39 + Methylthio + + + + 27 + + + 0 + + carboxyamidomethylation of K + 57.021464 + 57.0513 + 0 + + K + + 4 + Carbamidomethyl + + + + 28 + + + 0 + + carboxyamidomethylation of H + 57.021464 + 57.0513 + 0 + + H + + 4 + Carbamidomethyl + + + + 29 + + + 0 + + carboxyamidomethylation of D + 57.021464 + 57.0513 + 0 + + D + + 4 + Carbamidomethyl + + + + 30 + + + 0 + + carboxyamidomethylation of E + 57.021464 + 57.0513 + 0 + + E + + 4 + Carbamidomethyl + + + + 31 + + + 0 + + carbamylation of K + 43.005814 + 43.0247 + 0 + + K + + 5 + Carbamyl + + + + 32 + + + 5 + + carbamylation of n-term peptide + 43.005814 + 43.0247 + 0 + + X + + 5 + Carbamyl + + + + 33 + + + 0 + + citrullination of R + 0.984016 + 0.9848 + 0 + + R + + 7 + Deamidated + + + + 34 + + + 0 + + oxidation of C to cysteic acid + 47.984744 + 47.9982 + 0 + + C + + 345 + Trioxidation + + + + 35 + + + 0 + + di-iodination of Y + 251.793296 + 251.7931 + 0 + + Y + + 130 + Diiodo + + + + 36 + + + 0 + + di-methylation of K + 28.031300 + 28.0532 + 0 + + K + + 36 + Dimethyl + + + + 37 + + + 0 + + di-methylation of R + 28.031300 + 28.0532 + 0 + + R + + 36 + Dimethyl + + + + 38 + + + 5 + + di-methylation of peptide n-term + 28.031300 + 28.0532 + 0 + 36 + Dimethyl + + + + 39 + + + 0 + + oxidation of F to dihydroxyphenylalanine + 31.989829 + 31.9988 + 0 + + F + + 425 + Dioxidation + + + + 40 + + + 0 + + gammathiopropionylation of K + 87.998285 + 88.1283 + 0 + + K + + 126 + Thioacyl + + + + 41 + + + 5 + + gammathiopropionylation of peptide n-term + 87.998285 + 88.1283 + 0 + 126 + Thioacyl + + + + 42 + + + 0 + + farnesylation of C + 204.187801 + 204.3511 + 0 + + C + + 44 + Farnesyl + + + + 43 + + + 0 + + formylation of K + 27.994915 + 28.0101 + 0 + + K + + 122 + Formyl + + + + 44 + + + 5 + + formylation of peptide n-term + 27.994915 + 28.0101 + 0 + 122 + Formyl + + + + 45 + + + 0 + + oxidation of W to formylkynurenin + 31.989829 + 31.9988 + 0 + + W + + 425 + Dioxidation + + + + 46 + + + 0 + + fluorophenylalanine + 17.990578 + 17.9905 + 0 + + F + + 127 + Fluoro + + + + 47 + + + 0 + + beta-carboxylation of D + 43.989829 + 44.0095 + 0 + + D + + 299 + Carboxy + + + + 48 + + + 0 + + gamma-carboxylation of E + 43.989829 + 44.0095 + 0 + + E + + 299 + Carboxy + + + + 49 + + + 0 + + geranyl-geranyl + 272.250401 + 272.4681 + 0 + + C + + 48 + GeranylGeranyl + + + + 50 + + + 2 + + glucuronylation of protein n-term + 176.032088 + 176.1241 + 0 + + G + + 54 + Glucuronyl + + + + 51 + + + 0 + + glutathione disulfide + 305.068156 + 305.3076 + 0 + + C + + 55 + Glutathione + + + + 52 + + + 0 + + ubiquitinylation residue + 114.042927 + 114.1026 + 0 + + K + + 121 + GlyGly + + + + 53 + + + 0 + + guanidination of K + 42.021798 + 42.0400 + 0 + + K + + 52 + Guanidinyl + + + + 54 + + + 0 + + oxidation of H to N + -23.015984 + -23.0366 + 0 + + H + + 348 + His->Asn + + + + 55 + + + 0 + + oxidation of H to D + -22.031969 + -22.0519 + 0 + + D + + 349 + His->Asp + + + + 56 + + + 8 + + homoserine + -29.992806 + -30.0922 + 0 + + M + + 10 + Met->Hse + + + + 57 + + + 8 + + homoserine lactone + -48.003371 + -48.1075 + 0 + + M + + 11 + Met->Hsl + + + + 58 + + + 0 + + oxidation of W to hydroxykynurenin + 19.989829 + 19.9881 + 0 + + W + + 350 + Trp->Hydroxykynurenin + + + + 59 + + + 0 + + hydroxylation of D + 15.994915 + 15.9994 + 0 + + D + + 35 + Oxidation + + + + 60 + + + 0 + + hydroxylation of K + 15.994915 + 15.9994 + 0 + + K + + 35 + Oxidation + + + + 61 + + + 0 + + hydroxylation of N + 15.994915 + 15.9994 + 0 + + N + + 35 + Oxidation + + + + 62 + + + 0 + + hydroxylation of P + 15.994915 + 15.9994 + 0 + + P + + 35 + Oxidation + + + + 63 + + + 0 + + hydroxylation of F + 15.994915 + 15.9994 + 0 + + F + + 35 + Oxidation + + + + 64 + + + 0 + + hydroxylation of Y + 15.994915 + 15.9994 + 0 + + Y + + 35 + Oxidation + + + + 65 + + + 0 + + iodination of Y + 125.896648 + 125.8965 + 0 + + Y + + 129 + Iodo + + + + 66 + + + 0 + + oxidation of W to kynurenin + 3.994915 + 3.9887 + 0 + + W + + 351 + Trp->Kynurenin + + + + 67 + + + 0 + + lipoyl K + 188.032956 + 188.3103 + 0 + + K + + 42 + Lipoyl + + + + 68 + + + 7 + + methyl ester of peptide c-term (duplicate of 18) + 14.015650 + 14.0266 + 0 + 34 + Methyl + + + + 69 + + + 0 + + methyl ester of D + 14.015650 + 14.0266 + 0 + + D + + 34 + Methyl + + + + 70 + + + 0 + + methyl ester of E (duplicate of 17) + 14.015650 + 14.0266 + 0 + + E + + 34 + Methyl + + + + 71 + + + 0 + + methyl ester of S + 14.015650 + 14.0266 + 0 + + S + + 34 + Methyl + + + + 72 + + + 0 + + methyl ester of Y + 14.015650 + 14.0266 + 0 + + Y + + 34 + Methyl + + + + 73 + + + 0 + + methyl C + 14.015650 + 14.0266 + 0 + + C + + 34 + Methyl + + + + 74 + + + 0 + + methyl H + 14.015650 + 14.0266 + 0 + + H + + 34 + Methyl + + + + 75 + + + 0 + + methyl N + 14.015650 + 14.0266 + 0 + + N + + 34 + Methyl + + + + 76 + + + 5 + + methylation of peptide n-term + 14.015650 + 14.0266 + 0 + 34 + Methyl + + + + 77 + + + 0 + + methyl R + 14.015650 + 14.0266 + 0 + + R + + 34 + Methyl + + + + 78 + + + 2 + + myristoleylation of G + 208.182715 + 208.3398 + 0 + + G + + 134 + Myristoleyl + + + + 79 + + + 2 + + myristoyl-4H of G + 206.167065 + 206.3239 + 0 + + G + + 135 + Myristoyl+Delta:H(-4) + + + + 80 + + + 6 + + myristoylation of peptide n-term G + 210.198366 + 210.3556 + 0 + + G + + 45 + Myristoyl + + + + 81 + + + 0 + + myristoylation of K + 210.198366 + 210.3556 + 0 + + K + + 45 + Myristoyl + + + + 82 + + + 1 + + formylation of protein n-term + 27.994915 + 28.0101 + 0 + 122 + Formyl + + + + 83 + + + 0 + + NEM C + 125.047679 + 125.1253 + 0 + + C + + 108 + Nethylmaleimide + + + + 84 + + + 0 + + NIPCAM + 99.068414 + 99.1311 + 0 + + C + + 17 + NIPCAM + + + + 85 + + + 0 + + oxidation of W to nitro + 44.985078 + 44.9976 + 0 + + W + + 354 + Nitro + + + + 86 + + + 0 + + oxidation of Y to nitro + 44.985078 + 44.9976 + 0 + + Y + + 354 + Nitro + + + + 87 + + + 5 + + O18 on peptide n-term + 2.004246 + 1.9998 + 0 + 258 + Label:18O(1) + + + + 88 + + + 5 + + di-O18 on peptide n-term + 4.00849 + 3.9995 + 0 + 193 + Label:18O(2) + + + + 89 + + + 0 + + oxidation of H + 15.994915 + 15.9994 + 0 + + H + + 35 + Oxidation + + + + 90 + + + 0 + + oxidation of W + 15.994915 + 15.9994 + 0 + + W + + 35 + Oxidation + + + + 91 + + + 0 + + phosphopantetheine S + 340.085794 + 340.3330 + 0 + + S + + 49 + Phosphopantetheine + + + + 92 + + + 0 + + palmitoylation of C + 238.229666 + 238.4088 + 0 + + C + + 47 + Palmitoyl + + + + 93 + + + 0 + + palmitoylation of K + 238.229666 + 238.4088 + 0 + + K + + 47 + Palmitoyl + + + + 94 + + + 0 + + palmitoylation of S + 238.229666 + 238.4088 + 0 + + S + + 47 + Palmitoyl + + + + 95 + + + 0 + + palmitoylation of T + 238.229666 + 238.4088 + 0 + + T + + 47 + Palmitoyl + + + + 96 + + + 0 + + phosphorylation of S with prompt loss + -18.010565 + -18.0153 + 0 + + S + + 23 + Dehydrated + + + + 97 + + + 0 + + phosphorylation of T with prompt loss + -18.010565 + -18.0153 + 0 + + T + + 23 + Dehydrated + + + + 98 + + + 0 + + phosphorylation with prompt loss on Y + -18.010565 + -18.0153 + 0 + + Y + + 23 + Dehydrated + + + + 99 + + + 0 + + phosphorylation with neutral loss on C + 79.966331 + 79.9799 + 0 + + C + + + + 97.976896 + 97.9952 + 0 + + + 21 + Phospho + + + + 100 + + + 0 + + phosphorylation with neutral loss on D + 79.966331 + 79.9799 + 0 + + D + + + + 97.976896 + 97.9952 + 0 + + + 21 + Phospho + + + + 101 + + + 0 + + phosphorylation with neutral loss on H + 79.966331 + 79.9799 + 0 + + H + + + + 97.976896 + 97.9952 + 0 + + + 21 + Phospho + + + + 102 + + + 0 + + propionyl light K + 56.026215 + 56.0633 + 0 + + K + + 58 + Propionyl + + + + 103 + + + 5 + + propionyl light on peptide n-term + 56.026215 + 56.0633 + 0 + 58 + Propionyl + + + + 104 + + + 0 + + propionyl heavy K + 59.036279 + 59.0412 + 0 + + K + + 59 + Propionyl:13C(3) + + + + 105 + + + 5 + + propionyl heavy peptide n-term + 59.036279 + 59.0412 + 0 + 59 + Propionyl:13C(3) + + + + 106 + + + 0 + + pyridyl K + 119.037114 + 119.1207 + 0 + + K + + 25 + Pyridylacetyl + + + + 107 + + + 5 + + pyridyl peptide n-term + 119.037114 + 119.1207 + 0 + 25 + Pyridylacetyl + + + + 108 + + + 6 + + pyro-cmC + -17.026549 + -17.0305 + 0 + + C + + 385 + Ammonia-loss + + + + 109 + + + 6 + + pyro-glu from n-term E + -18.010565 + -18.0153 + 0 + + E + + 27 + Glu->pyro-Glu + + + + 110 + + + 6 + + pyro-glu from n-term Q + -17.026549 + -17.0305 + 0 + + Q + + 385 + Ammonia-loss + + + + 111 + + + 0 + + oxidation of P to pyroglutamic acid + 13.979265 + 13.9835 + 0 + + P + + 359 + Pro->pyro-Glu + + + + 112 + + + 0 + + s-pyridylethylation of C + 105.057849 + 105.1372 + 0 + + C + + 31 + Pyridylethyl + + + + 113 + + + 0 + + SeMet + 47.944449 + 46.8950 + 0 + + M + + 162 + Delta:S(-1)Se(1) + + + + 114 + + + 0 + + sulfation of Y + 79.956815 + 80.0632 + 0 + + Y + + 40 + Sulfo + + + + 115 + + + 0 + + sulphone of M + 31.989829 + 31.9988 + 0 + + M + + 425 + Dioxidation + + + + 116 + + + 0 + + tri-iodination of Y + 377.689944 + 377.6896 + 0 + + Y + + 131 + Triiodo + + + + 117 + + + 0 + + tri-methylation of R + 42.046950 + 42.0797 + 0 + + R + + 37 + Trimethyl + + + + 118 + + + 6 + + n-acyl diglyceride cysteine + 788.725777 + 789.3049 + 0 + + C + + 51 + Tripalmitate + + + + 129 + + + 0 + + ICAT light + 227.126991 + 227.2603 + 0 + + C + + 105 + ICAT-C + + + + 130 + + + 0 + + ICAT heavy + 236.157185 + 236.1942 + 0 + + C + + 106 + ICAT-C:13C(9) + + + + 131 + + + 0 + + CAMthiopropanoyl K + 145.019749 + 145.1796 + 0 + + K + + 293 + CAMthiopropanoyl + + + + 132 + + + 0 + + phosphorylation with neutral loss on S + 79.966331 + 79.9799 + 0 + + S + + + + 97.976896 + 97.9952 + 0 + + + 21 + Phospho + + + + 133 + + + 0 + + phosphorylation with neutral loss on T + 79.966331 + 79.9799 + 0 + + T + + + + 97.976896 + 97.9952 + 0 + + + 21 + Phospho + + + + 134 + + + 0 + + phosphorylation of S with ETD loss + 79.966331 + 79.9799 + 0 + + S + + + + 2.016 + 2.016 + 0 + + + + + + 135 + + + 0 + + phosphorylation of T with ETD loss + 79.966331 + 79.9799 + 0 + + T + + + + 2.016 + 2.016 + 0 + + + + + + 136 + + + 0 + + heavy arginine-13C6 + 6.020129 + 5.9559 + 0 + + R + + 188 + Label:13C(6) + + + + 137 + + + 0 + + heavy arginine-13C6-15N4 + 10.008269 + 9.9296 + 0 + + R + + 267 + Label:13C(6)15N(4) + + + + 138 + + + 0 + + heavy lysine-13C6 + 6.020129 + 5.9559 + 0 + + K + + 188 + Label:13C(6) + + + + 139 + + + 6 + + PNGasF in O18 water + 2.988261 + 2.9845 + 0 + + N + + 366 + Deamidated:18O(1) + + + + 140 + + + 0 + + beta elimination of S + -18.010565 + -18.0153 + 0 + + S + + 23 + Dehydrated + + + + 141 + + + 0 + + beta elimination of T + -18.010565 + -18.0153 + 0 + + T + + 23 + Dehydrated + + + + 162 + + + 0 + + oxidation of C to sulfinic acid + 31.989829 + 31.9988 + 0 + + C + + 425 + Dioxidation + + + + 163 + + + 0 + + arginine to ornithine + -42.021798 + -42.0400 + 0 + + R + + 372 + Arg->Orn + + + + 164 + + + 0 + + dehydro of S and T + -18.010565 + -18.0153 + 0 + + S + T + + 23 + Dehydrated + + + + 165 + + + 0 + + carboxykynurenin of W + 47.98474389 + 47.9979141 + 0 + + W + + + + + 166 + + + 0 + + sumoylation of K + 484.2282 + 0 + 0 + + K + + 846 + + + + 167 + + + 5 + + iTRAQ114 on nterm + 144.105918 + 144.1680 + 0 + 532 + iTRAQ4plex114 + + + + 168 + + + 0 + + iTRAQ114 on K + 144.105918 + 144.1680 + 0 + + K + + 532 + iTRAQ4plex114 + + + + 169 + + + 0 + + iTRAQ114 on Y + 144.105918 + 144.1680 + 0 + + Y + + 532 + iTRAQ4plex114 + + + + 170 + + + 5 + + iTRAQ115 on nterm + 144.099599 + 144.1688 + 0 + 533 + iTRAQ4plex115 + + + + 171 + + + 0 + + iTRAQ115 on K + 144.099599 + 144.1688 + 0 + + K + + 533 + iTRAQ4plex115 + + + + 172 + + + 0 + + iTRAQ115 on Y + 144.099599 + 144.1688 + 0 + + Y + + 533 + iTRAQ4plex115 + + + + 173 + + + 5 + + iTRAQ116 on nterm + 144.102063 + 144.1544 + 0 + 214 + iTRAQ4plex + + + + 174 + + + 0 + + iTRAQ116 on K + 144.102063 + 144.1544 + 0 + + K + + 214 + iTRAQ4plex + + + + 175 + + + 0 + + iTRAQ116 on Y + 144.102063 + 144.1544 + 0 + + Y + + 214 + iTRAQ4plex + + + + 176 + + + 5 + + iTRAQ117 on nterm + 144.102063 + 144.1544 + 0 + 214 + iTRAQ4plex + + + + 177 + + + 0 + + iTRAQ117 on K + 144.102063 + 144.1544 + 0 + + K + + 214 + iTRAQ4plex + + + + 178 + + + 0 + + iTRAQ117 on Y + 144.102063 + 144.1544 + 0 + + Y + + 214 + iTRAQ4plex + + + + 179 + + + 0 + + MMTS on C + 45.987721 + 46.0916 + 0 + + C + + 39 + Methylthio + + + + 180 + + + 0 + + heavy lysine - 2H4 + 4.025107 + 4.0246 + 0 + + K + + 481 + Label:2H(4) + + + + 181 + + + 0 + + heavy lysine - 13C6 15N2 + 8.014199 + 7.9427 + 0 + + K + + 259 + Label:13C(6)15N(2) + + + + 182 + + + 0 + + Asparagine HexNAc + 203.079373 + 203.1925 + 0 + + N + + 43 + HexNAc + + + + 183 + + + 0 + + Asparagine dHexHexNAc + 349.137281 + 349.3337 + 0 + + N + + 142 + HexNAc(1)dHex(1) + + + + 184 + + + 0 + + Serine HexNAc + 203.079373 + 203.1925 + 0 + + S + + 43 + HexNAc + + + + 185 + + + 0 + + Threonine HexNAc + 203.079373 + 203.1925 + 0 + + T + + 43 + HexNAc + + + + 186 + + + 0 + + palmitoleyl of S + 236.214016 + 236.3929 + 0 + + S + + 431 + Palmitoleyl + + + + 187 + + + 0 + + palmitoleyl of C + 236.214016 + 236.3929 + 0 + + C + + 431 + Palmitoleyl + + + + 188 + + + 0 + + palmitoleyl of T + 236.214016 + 236.3929 + 0 + + T + + 431 + Palmitoleyl + + + + 189 + + + 0 + + CHD2-di-methylation of K + 32.056407 + 32.0778 + 0 + + K + + 199 + Dimethyl:2H(4) + + + + 190 + + + 5 + + CHD2-di-methylation of peptide n-term + 32.056407 + 32.0778 + 0 + 199 + Dimethyl:2H(4) + + + + 191 + + + 0 + + Maleimide-PEO2-Biotin of C + 525.225719 + 525.6183 + 0 + + C + + 522 + Maleimide-PEO2-Biotin + + + + 192 + + + 0 + + phosphorylation of H + 79.966331 + 79.9799 + 0 + + H + + 21 + Phospho + + + + 193 + + + 0 + + oxidation of C + 15.994915 + 15.9994 + 0 + + C + + 35 + Oxidation + + + + 194 + + + 0 + + oxidation of Y (duplicate of 64) + 15.994915 + 15.9994 + 0 + + Y + + 35 + Oxidation + + + + 195 + + + 0 + + Uniblue A on K + 484.039891 + 484.5016 + 0 + + K + + + + + 196 + + + 0 + + deamidation of N + 0.984016 + 0.9848 + 0 + + N + + 7 + Deamidated + + + + 197 + + + 0 + + trideuteration of L (SILAC) + 3.018830 + 3.0185 + 0 + + L + + 262 + Label:2H(3) + + + + 198 + + + 0 + + TMT duplex on K + 225.155833 + 225.2921 + 0 + + K + + 738 + + + + 199 + + + 5 + + TMT duplex on n-term peptide + 225.155833 + 225.2921 + 0 + + X + + 738 + + + + 198 + + + 0 + + TMT 6-plex on K + 229.162932 + 229.2634 + 0 + + K + + 738 + + + + 199 + + + 5 + + TMT 6-plex on n-term peptide + 229.162932 + 229.2634 + 0 + + X + + 738 + + + + 200 + + + 5 + + iTRAQ8plex:13C(7)15N(1) on nterm + 304.205360 + 304.3074 + 0 + 730 + + + + 201 + + + 0 + + iTRAQ8plex:13C(7)15N(1) on K + 304.205360 + 304.3074 + 0 + + K + + 730 + + + + 202 + + + 0 + + iTRAQ8plex:13C(7)15N(1) on Y + 304.205360 + 304.3074 + 0 + + Y + + 730 + + + + 203 + + + 5 + + iTRAQ8plex:13C(6)15N(2) on nterm + 304.199040 + 304.3081 + 0 + 731 + + + + 204 + + + 0 + + iTRAQ8plex:13C(6)15N(2) on K + 304.199040 + 304.3081 + 0 + + K + + 731 + + + + 205 + + + 0 + + iTRAQ8plex:13C(6)15N(2) on Y + 304.199040 + 304.3081 + 0 + + Y + + 731 + + + + 206 + + + 0 + + selenocysteine + 47.944449 + 46.8950 + 0 + + C + + 162 + + + + 207 + + + 0 + + carboxymethylated selenocysteine + 105.949928 + 104.9311 + 0 + + C + + + diff -r 000000000000 -r 0578e296cab4 searchGUI_usermods.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchGUI_usermods.xml Fri May 10 17:58:22 2013 -0400 @@ -0,0 +1,455 @@ + + + + + + 119 + + + 5 + + dimethyl 2d n-terminus + 32.0564 + 0 + 0 + + + + 120 + + + 0 + + dimethyl 2d k + 32.0564 + 0 + 0 + + K + + + + + 121 + + + 0 + + gtp desthiobiotinc12 + 196.121178 + 0 + 0 + + K + + + + + 122 + + + 0 + + gtp desthiobiotinc13 + 202.141307 + 0 + 0 + + K + + + + + 123 + + + 0 + + User modification 5 + 0 + 0 + 0 + + X + + + + + 124 + + + 0 + + User modification 6 + 0 + 0 + 0 + + X + + + + + 125 + + + 0 + + User modification 7 + 0 + 0 + 0 + + X + + + + + 126 + + + 0 + + User modification 8 + 0 + 0 + 0 + + X + + + + + 127 + + + 0 + + User modification 9 + 0 + 0 + 0 + + X + + + + + 128 + + + 0 + + User modification 10 + 0 + 0 + 0 + + X + + + + + 142 + + + 0 + + User modification 11 + 0 + 0 + 0 + + X + + + + + 143 + + + 0 + + User modification 12 + 0 + 0 + 0 + + X + + + + + 144 + + + 0 + + User modification 13 + 0 + 0 + 0 + + X + + + + + 145 + + + 0 + + User modification 14 + 0 + 0 + 0 + + X + + + + + 146 + + + 0 + + User modification 15 + 0 + 0 + 0 + + X + + + + + 147 + + + 0 + + User modification 16 + 0 + 0 + 0 + + X + + + + + 148 + + + 0 + + User modification 17 + 0 + 0 + 0 + + X + + + + + 149 + + + 0 + + User modification 18 + 0 + 0 + 0 + + X + + + + + 150 + + + 0 + + User modification 19 + 0 + 0 + 0 + + X + + + + + 151 + + + 0 + + User modification 20 + 0 + 0 + 0 + + X + + + + + 152 + + + 0 + + User modification 21 + 0 + 0 + 0 + + X + + + + + 153 + + + 0 + + User modification 22 + 0 + 0 + 0 + + X + + + + + 154 + + + 0 + + User modification 23 + 0 + 0 + 0 + + X + + + + + 155 + + + 0 + + User modification 24 + 0 + 0 + 0 + + X + + + + + 156 + + + 0 + + User modification 25 + 0 + 0 + 0 + + X + + + + + 157 + + + 0 + + User modification 26 + 0 + 0 + 0 + + X + + + + + 158 + + + 0 + + User modification 27 + 0 + 0 + 0 + + X + + + + + 159 + + + 0 + + User modification 28 + 0 + 0 + 0 + + X + + + + + 160 + + + 0 + + User modification 29 + 0 + 0 + 0 + + X + + + + + 161 + + + 0 + + User modification 30 + 0 + 0 + 0 + + X + + + \ No newline at end of file diff -r 000000000000 -r 0578e296cab4 searchgui_mods.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchgui_mods.loc Fri May 10 17:58:22 2013 -0400 @@ -0,0 +1,210 @@ +methylation of k +oxidation of m +carboxymethyl c +carbamidomethyl c +deamidation of n and q +propionamide c +phosphorylation of s +phosphorylation of t +phosphorylation of y +m cleavage from protein n-term +acetylation of protein n-term +methylation of protein n-term +tri-methylation of protein n-term +beta methythiolation of d +methylation of q +tri-methylation of k +methylation of d +methylation of e +methylation of peptide c-term +tri-deuteromethylation of d +tri-deuteromethylation of e +tri-deuteromethylation of peptide c-term +n-formyl met addition +2-amino-3-oxo-butanoic acid t +acetylation of k +amidation of peptide c-term +beta-methylthiolation of d (duplicate of 13) +carboxyamidomethylation of k +carboxyamidomethylation of h +carboxyamidomethylation of d +carboxyamidomethylation of e +carbamylation of k +carbamylation of n-term peptide +citrullination of r +oxidation of c to cysteic acid +di-iodination of y +di-methylation of k +di-methylation of r +di-methylation of peptide n-term +oxidation of f to dihydroxyphenylalanine +gammathiopropionylation of k +gammathiopropionylation of peptide n-term +farnesylation of c +formylation of k +formylation of peptide n-term +oxidation of w to formylkynurenin +fluorophenylalanine +beta-carboxylation of d +gamma-carboxylation of e +geranyl-geranyl +glucuronylation of protein n-term +glutathione disulfide +ubiquitinylation residue +guanidination of k +oxidation of h to n +oxidation of h to d +homoserine +homoserine lactone +oxidation of w to hydroxykynurenin +hydroxylation of d +hydroxylation of k +hydroxylation of n +hydroxylation of p +hydroxylation of f +hydroxylation of y +iodination of y +oxidation of w to kynurenin +lipoyl k +methyl ester of peptide c-term (duplicate of 18) +methyl ester of d +methyl ester of e (duplicate of 17) +methyl ester of s +methyl ester of y +methyl c +methyl h +methyl n +methylation of peptide n-term +methyl r +myristoleylation of g +myristoyl-4h of g +myristoylation of peptide n-term g +myristoylation of k +formylation of protein n-term +nem c +nipcam +oxidation of w to nitro +oxidation of y to nitro +o18 on peptide n-term +di-o18 on peptide n-term +oxidation of h +oxidation of w +phosphopantetheine s +palmitoylation of c +palmitoylation of k +palmitoylation of s +palmitoylation of t +phosphorylation of s with prompt loss +phosphorylation of t with prompt loss +phosphorylation with prompt loss on y +phosphorylation with neutral loss on c +phosphorylation with neutral loss on d +phosphorylation with neutral loss on h +propionyl light k +propionyl light on peptide n-term +propionyl heavy k +propionyl heavy peptide n-term +pyridyl k +pyridyl peptide n-term +pyro-cmc +pyro-glu from n-term e +pyro-glu from n-term q +oxidation of p to pyroglutamic acid +s-pyridylethylation of c +semet +sulfation of y +sulphone of m +tri-iodination of y +tri-methylation of r +n-acyl diglyceride cysteine +icat light +icat heavy +camthiopropanoyl k +phosphorylation with neutral loss on s +phosphorylation with neutral loss on t +phosphorylation of s with etd loss +phosphorylation of t with etd loss +heavy arginine-13c6 +heavy arginine-13c6-15n4 +heavy lysine-13c6 +pngasf in o18 water +beta elimination of s +beta elimination of t +oxidation of c to sulfinic acid +arginine to ornithine +dehydro of s and t +carboxykynurenin of w +sumoylation of k +itraq114 on nterm +itraq114 on k +itraq114 on y +itraq115 on nterm +itraq115 on k +itraq115 on y +itraq116 on nterm +itraq116 on k +itraq116 on y +itraq117 on nterm +itraq117 on k +itraq117 on y +mmts on c +heavy lysine - 2h4 +heavy lysine - 13c6 15n2 +asparagine hexnac +asparagine dhexhexnac +serine hexnac +threonine hexnac +palmitoleyl of s +palmitoleyl of c +palmitoleyl of t +chd2-di-methylation of k +chd2-di-methylation of peptide n-term +maleimide-peo2-biotin of c +phosphorylation of h +oxidation of c +oxidation of y (duplicate of 64) +uniblue a on k +deamidation of n +trideuteration of l (silac) +tmt duplex on k +tmt duplex on n-term peptide +tmt 6-plex on k +tmt 6-plex on n-term peptide +itraq8plex:13c(7)15n(1) on nterm +itraq8plex:13c(7)15n(1) on k +itraq8plex:13c(7)15n(1) on y +itraq8plex:13c(6)15n(2) on nterm +itraq8plex:13c(6)15n(2) on k +itraq8plex:13c(6)15n(2) on y +selenocysteine +carboxymethylated selenocysteine +dimethyl 2d n-terminus +dimethyl 2d k +gtp desthiobiotinc12 +gtp desthiobiotinc13 +user modification 5 +user modification 6 +user modification 7 +user modification 8 +user modification 9 +user modification 10 +user modification 11 +user modification 12 +user modification 13 +user modification 14 +user modification 15 +user modification 16 +user modification 17 +user modification 18 +user modification 19 +user modification 20 +user modification 21 +user modification 22 +user modification 23 +user modification 24 +user modification 25 +user modification 26 +user modification 27 +user modification 28 +user modification 29 +user modification 30 diff -r 000000000000 -r 0578e296cab4 searchgui_mods.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchgui_mods.loc.sample Fri May 10 17:58:22 2013 -0400 @@ -0,0 +1,210 @@ +methylation of k +oxidation of m +carboxymethyl c +carbamidomethyl c +deamidation of n and q +propionamide c +phosphorylation of s +phosphorylation of t +phosphorylation of y +m cleavage from protein n-term +acetylation of protein n-term +methylation of protein n-term +tri-methylation of protein n-term +beta methythiolation of d +methylation of q +tri-methylation of k +methylation of d +methylation of e +methylation of peptide c-term +tri-deuteromethylation of d +tri-deuteromethylation of e +tri-deuteromethylation of peptide c-term +n-formyl met addition +2-amino-3-oxo-butanoic acid t +acetylation of k +amidation of peptide c-term +beta-methylthiolation of d (duplicate of 13) +carboxyamidomethylation of k +carboxyamidomethylation of h +carboxyamidomethylation of d +carboxyamidomethylation of e +carbamylation of k +carbamylation of n-term peptide +citrullination of r +oxidation of c to cysteic acid +di-iodination of y +di-methylation of k +di-methylation of r +di-methylation of peptide n-term +oxidation of f to dihydroxyphenylalanine +gammathiopropionylation of k +gammathiopropionylation of peptide n-term +farnesylation of c +formylation of k +formylation of peptide n-term +oxidation of w to formylkynurenin +fluorophenylalanine +beta-carboxylation of d +gamma-carboxylation of e +geranyl-geranyl +glucuronylation of protein n-term +glutathione disulfide +ubiquitinylation residue +guanidination of k +oxidation of h to n +oxidation of h to d +homoserine +homoserine lactone +oxidation of w to hydroxykynurenin +hydroxylation of d +hydroxylation of k +hydroxylation of n +hydroxylation of p +hydroxylation of f +hydroxylation of y +iodination of y +oxidation of w to kynurenin +lipoyl k +methyl ester of peptide c-term (duplicate of 18) +methyl ester of d +methyl ester of e (duplicate of 17) +methyl ester of s +methyl ester of y +methyl c +methyl h +methyl n +methylation of peptide n-term +methyl r +myristoleylation of g +myristoyl-4h of g +myristoylation of peptide n-term g +myristoylation of k +formylation of protein n-term +nem c +nipcam +oxidation of w to nitro +oxidation of y to nitro +o18 on peptide n-term +di-o18 on peptide n-term +oxidation of h +oxidation of w +phosphopantetheine s +palmitoylation of c +palmitoylation of k +palmitoylation of s +palmitoylation of t +phosphorylation of s with prompt loss +phosphorylation of t with prompt loss +phosphorylation with prompt loss on y +phosphorylation with neutral loss on c +phosphorylation with neutral loss on d +phosphorylation with neutral loss on h +propionyl light k +propionyl light on peptide n-term +propionyl heavy k +propionyl heavy peptide n-term +pyridyl k +pyridyl peptide n-term +pyro-cmc +pyro-glu from n-term e +pyro-glu from n-term q +oxidation of p to pyroglutamic acid +s-pyridylethylation of c +semet +sulfation of y +sulphone of m +tri-iodination of y +tri-methylation of r +n-acyl diglyceride cysteine +icat light +icat heavy +camthiopropanoyl k +phosphorylation with neutral loss on s +phosphorylation with neutral loss on t +phosphorylation of s with etd loss +phosphorylation of t with etd loss +heavy arginine-13c6 +heavy arginine-13c6-15n4 +heavy lysine-13c6 +pngasf in o18 water +beta elimination of s +beta elimination of t +oxidation of c to sulfinic acid +arginine to ornithine +dehydro of s and t +carboxykynurenin of w +sumoylation of k +itraq114 on nterm +itraq114 on k +itraq114 on y +itraq115 on nterm +itraq115 on k +itraq115 on y +itraq116 on nterm +itraq116 on k +itraq116 on y +itraq117 on nterm +itraq117 on k +itraq117 on y +mmts on c +heavy lysine - 2h4 +heavy lysine - 13c6 15n2 +asparagine hexnac +asparagine dhexhexnac +serine hexnac +threonine hexnac +palmitoleyl of s +palmitoleyl of c +palmitoleyl of t +chd2-di-methylation of k +chd2-di-methylation of peptide n-term +maleimide-peo2-biotin of c +phosphorylation of h +oxidation of c +oxidation of y (duplicate of 64) +uniblue a on k +deamidation of n +trideuteration of l (silac) +tmt duplex on k +tmt duplex on n-term peptide +tmt 6-plex on k +tmt 6-plex on n-term peptide +itraq8plex:13c(7)15n(1) on nterm +itraq8plex:13c(7)15n(1) on k +itraq8plex:13c(7)15n(1) on y +itraq8plex:13c(6)15n(2) on nterm +itraq8plex:13c(6)15n(2) on k +itraq8plex:13c(6)15n(2) on y +selenocysteine +carboxymethylated selenocysteine +dimethyl 2d n-terminus +dimethyl 2d k +gtp desthiobiotinc12 +gtp desthiobiotinc13 +user modification 5 +user modification 6 +user modification 7 +user modification 8 +user modification 9 +user modification 10 +user modification 11 +user modification 12 +user modification 13 +user modification 14 +user modification 15 +user modification 16 +user modification 17 +user modification 18 +user modification 19 +user modification 20 +user modification 21 +user modification 22 +user modification 23 +user modification 24 +user modification 25 +user modification 26 +user modification 27 +user modification 28 +user modification 29 +user modification 30 diff -r 000000000000 -r 0578e296cab4 update.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/update.sh Fri May 10 17:58:22 2013 -0400 @@ -0,0 +1,35 @@ +#!/bin/bash + +LICENSE_FILE=LICENSE +# Ensure repository contains license file. +if [ ! -e "$LICENSE_FILE" ]; +then + wget http://www.apache.org/licenses/LICENSE-2.0.txt -O "$LICENSE_FILE" +fi + +# Run repository specific update actions. +if [ -f update_repo.sh ]; +then + ./update_repo.sh +fi + +wget https://raw.github.com/gist/3749747/README_GALAXYP.md -O README_GALAXYP.md + +# Create repository README +if [ ! -e README_REPO.md ]; +then + echo "TODO: Document this tool repository." > README_REPO.md +fi +cat README_REPO.md README_GALAXYP.md > README.md + + +# If version file exists, update all tools to this version +VERSION_FILE=version +if [ -e "$VERSION_FILE" ]; +then + VERSION=`cat $VERSION_FILE` + + # Replace tool version in each tool XML file ` + find -iname "*xml" -exec sed -i'' -e '0,/version="\(.\+\)"/s/version="\(.\+\)"/version="'$VERSION'"/1g' {} \; + +fi