docker package dev environment

docker/.tral/config.ini

@@ -0,0 +1,102 @@
+sequence_type = AA
+
+[sequence]
+    [[repeat_detection]]
+        # AA includes all detectors used by default on protein sequence data.
+        AA = HHrepID, T-REKS, TRUST, XSTREAM
+        # DNA includes all detectors used by default on protein sequence data.
+        DNA = Phobos, TRED, T-REKS, TRF, XSTREAM
+    [[repeat_detector_path]]
+        # If the executable is in the system path, supply its name. Otherwise, supply the full path to the executable. Details are explained in TRAL's online docs.
+        PHOBOS = phobos
+        HHrepID = hhrepid_64
+        HHrepID_dummyhmm = /.tral/data/hhrepid/dummyHMM.hmm
+        T-REKS = T-REKS
+        TRED = tred
+        TRF = trf
+        TRUST = TRUST
+        TRUST_substitutionmatrix = /tral/tral_external_software/TRUST_Align/Align/BLOSUM50
+        XSTREAM = XSTREAM
+
+[hmm]
+    hmmbuild = hmmbuild
+    l_effective_max = 50
+
+[filter]
+    [[basic]]
+        tag = basic_filter
+        [[[dict]]]
+            [[[[pvalue]]]]
+                func_name = pvalue
+                score = phylo_gap01
+                threshold = 0.1
+            [[[[n_effective]]]]
+                func_name = attribute
+                attribute = n_effective
+                type = min
+                threshold = 1.9
+
+[repeat]
+    scoreslist = phylo_gap01, # score (the comma in the end is needed for TRAL)
+    calc_score = False # is the score calculated?
+    calc_pvalue = False # is the pvalue calculated?
+    precision = 10
+    ginsi = ginsi # integrated in MAFFT
+	Castor = Castor
+    [[castor_parameter]]
+        rate_distribution = constant # either constant or gamma
+    alfsim = alfsim
+
+[repeat_list]
+    # Columns to include in repeat list TSV output
+    # Allowed values:
+    # - begin: position of the tandem repeats within the sequence,
+    # - pvalue: statistical significance of the tandem repeats
+    # - divergence: divergence of the tandem repeat units
+    # - l_effective: length of the tandem repeat units
+    # - n_effective: number of tandem repeat units
+    # - msa_original: multiple sequence alignment
+    # - score: score corresponding to the value of 'model'
+    # - repeat_region_length: total length of repeat region
+    output_characteristics = begin, msa_original, l_effective, n_effective, repeat_region_length, divergence, pvalue
+
+    # model for scoring repeats. Supported: entropy, parsimony, pSim, phylo, phylo_gap01, phylo_gap001
+    model = phylo_gap01
+
+[repeat_score]
+    evolutionary_model = lg
+    [[indel]]
+        indel_rate_per_site = 0.01
+        ignore_gaps = True
+        gaps = row_wise
+        zipf = 1.821
+    [[optimisation]]
+        start_min = 0.5
+        start_max = 1.5
+        n_iteration = 14
+    [[K80]]
+        kappa = 2.59
+    [[TN93]]
+        alpha_1 = 0.3
+        alpha_2 = 0.4
+        beta = 0.7
+    [[score_calibration]]
+        scoreslist=phylo_gap01, # score (the comma at the end is needed)
+        save_calibration = False
+        precision = 10
+
+[AA]
+    standard_chars = A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y
+    all_chars = A, B, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z
+    [[ambiguous_chars]]
+        B = D,N
+        O = K,
+        U = C,
+        Z = E,Q
+        X = A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y
+[DNA]
+    standard_chars = A, C, G, T
+    all_chars = A, C, G, T, N, X
+    [[ambiguous_chars]]
+        N = A, C, G, T
+        X = A, C, G, T

docker/.tral/data/ALF/jtt.dat

@@ -0,0 +1,50 @@
+0.531678 
+0.557967 0.451095 
+0.827445 0.154899 5.549530 
+0.574478 1.019843 0.313311 0.105625 
+0.556725 3.021995 0.768834 0.521646 0.091304 
+1.066681 0.318483 0.578115 7.766557 0.053907 3.417706 
+1.740159 1.359652 0.773313 1.272434 0.546389 0.231294 1.115632 
+0.219970 3.210671 4.025778 1.032342 0.724998 5.684080 0.243768 0.201696 
+0.361684 0.239195 0.491003 0.115968 0.150559 0.078270 0.111773 0.053769 0.181788 
+0.310007 0.372261 0.137289 0.061486 0.164593 0.709004 0.097485 0.069492 0.540571 2.335139 
+0.369437 6.529255 2.529517 0.282466 0.049009 2.966732 1.731684 0.269840 0.525096 0.202562 0.146481 
+0.469395 0.431045 0.330720 0.190001 0.409202 0.456901 0.175084 0.130379 0.329660 4.831666 3.856906 0.624581 
+0.138293 0.065314 0.073481 0.032522 0.678335 0.045683 0.043829 0.050212 0.453428 0.777090 2.500294 0.024521 0.436181 
+1.959599 0.710489 0.121804 0.127164 0.123653 1.608126 0.191994 0.208081 1.141961 0.098580 1.060504 0.216345 0.164215 0.148483 
+3.887095 1.001551 5.057964 0.589268 2.155331 0.548807 0.312449 1.874296 0.743458 0.405119 0.592511 0.474478 0.285564 0.943971 2.788406 
+4.582565 0.650282 2.351311 0.425159 0.469823 0.523825 0.331584 0.316862 0.477355 2.553806 0.272514 0.965641 2.114728 0.138904 1.176961 4.777647 
+0.084329 1.257961 0.027700 0.057466 1.104181 0.172206 0.114381 0.544180 0.128193 0.134510 0.530324 0.089134 0.201334 0.537922 0.069965 0.310927 0.080556 
+0.139492 0.235601 0.700693 0.453952 2.114852 0.254745 0.063452 0.052500 5.848400 0.303445 0.241094 0.087904 0.189870 5.484236 0.113850 0.628608 0.201094 0.747889 
+2.924161 0.171995 0.164525 0.315261 0.621323 0.179771 0.465271 0.470140 0.121827 9.533943 1.761439 0.124066 3.038533 0.593478 0.211561 0.408532 1.143980 0.239697 0.165473 
+
+
+0.076862 0.051057 0.042546 0.051269 0.020279 0.041061 0.061820 0.074714 0.022983 0.052569 0.091111 0.059498 0.023414 0.040530 0.050532 0.068225 0.058518 0.014336 0.032303 0.066374
+
+
+ A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V
+Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
+
+
+JTT rate matrix prepared using the DCMut method*
+------------------------------------------------
+
+The first part above indicates the symmetric 'exchangeability' parameters s_ij, 
+where s_ij = s_ji.
+The second part gives the amino acid equilibrium frequencies pi_i. 
+The net replacement rate from i to j is q_ij = pi_j*s_ij.
+
+This model is usually scaled so that the mean rate of change at
+equilibrium, Sum_i Sum_j!=i pi_i*q_ij, equals 1.  You should check this
+scaling before using the matrix above.  The PAML package will perform
+this scaling.
+
+//
+
+*Prepared by Carolin Kosiol and Nick Goldman, December 2003.
+
+See the following paper for more details:
+Kosiol, C., and Goldman, N. 2005. Different versions of the Dayhoff rate matrix. 
+Molecular Biology and Evolution 22:193-199.
+
+See also http://www.ebi.ac.uk/goldman/dayhoff

docker/.tral/data/ALF/lg.dat

@@ -0,0 +1,39 @@
+0.425093 
+0.276818 0.751878 
+0.395144 0.123954 5.076149 
+2.489084 0.534551 0.528768 0.062556 
+0.969894 2.807908 1.695752 0.523386 0.084808 
+1.038545 0.363970 0.541712 5.243870 0.003499 4.128591 
+2.066040 0.390192 1.437645 0.844926 0.569265 0.267959 0.348847 
+0.358858 2.426601 4.509238 0.927114 0.640543 4.813505 0.423881 0.311484 
+0.149830 0.126991 0.191503 0.010690 0.320627 0.072854 0.044265 0.008705 0.108882 
+0.395337 0.301848 0.068427 0.015076 0.594007 0.582457 0.069673 0.044261 0.366317 4.145067 
+0.536518 6.326067 2.145078 0.282959 0.013266 3.234294 1.807177 0.296636 0.697264 0.159069 0.137500 
+1.124035 0.484133 0.371004 0.025548 0.893680 1.672569 0.173735 0.139538 0.442472 4.273607 6.312358 0.656604 
+0.253701 0.052722 0.089525 0.017416 1.105251 0.035855 0.018811 0.089586 0.682139 1.112727 2.592692 0.023918 1.798853 
+1.177651 0.332533 0.161787 0.394456 0.075382 0.624294 0.419409 0.196961 0.508851 0.078281 0.249060 0.390322 0.099849 0.094464 
+4.727182 0.858151 4.008358 1.240275 2.784478 1.223828 0.611973 1.739990 0.990012 0.064105 0.182287 0.748683 0.346960 0.361819 1.338132 
+2.139501 0.578987 2.000679 0.425860 1.143480 1.080136 0.604545 0.129836 0.584262 1.033739 0.302936 1.136863 2.020366 0.165001 0.571468 6.472279 
+0.180717 0.593607 0.045376 0.029890 0.670128 0.236199 0.077852 0.268491 0.597054 0.111660 0.619632 0.049906 0.696175 2.457121 0.095131 0.248862 0.140825 
+0.218959 0.314440 0.612025 0.135107 1.165532 0.257336 0.120037 0.054679 5.306834 0.232523 0.299648 0.131932 0.481306 7.803902 0.089613 0.400547 0.245841 3.151815 
+2.547870 0.170887 0.083688 0.037967 1.959291 0.210332 0.245034 0.076701 0.119013 10.649107 1.702745 0.185202 1.898718 0.654683 0.296501 0.098369 2.188158 0.189510 0.249313 
+
+0.079066 0.055941 0.041977 0.053052 0.012937 0.040767 0.071586 0.057337 0.022355 0.062157 0.099081 0.064600 0.022951 0.042302 0.044040 0.061197 0.053287 0.012066 0.034155 0.069147 
+
+ A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V
+Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
+
+	Symmetrical part of the rate matrix and aa frequencies,
+estimated from 3905 globular protein amino acid sequences forming 182
+protein families.
+	The first part above indicates the symmetric 'exchangeability'
+parameters, where s_ij = s_ji.  The s_ij above are not scaled, but the
+PAML package will perform this scaling.
+	The second part gives the amino acid frequencies (pi_i)
+estimated from the 3905 sequences.  The net replacement rate from i to
+j is Q_ij = s_ij*pi_j.
+
+
+Citation:
+
+Le, S. Q., and O. Gascuel. 2008. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25:1307-1320.

docker/.tral/data/ALF/lg_FHuman.dat

@@ -0,0 +1,40 @@
+0.425093 
+0.276818 0.751878 
+0.395144 0.123954 5.076149 
+2.489084 0.534551 0.528768 0.062556 
+0.969894 2.807908 1.695752 0.523386 0.084808 
+1.038545 0.363970 0.541712 5.243870 0.003499 4.128591 
+2.066040 0.390192 1.437645 0.844926 0.569265 0.267959 0.348847 
+0.358858 2.426601 4.509238 0.927114 0.640543 4.813505 0.423881 0.311484 
+0.149830 0.126991 0.191503 0.010690 0.320627 0.072854 0.044265 0.008705 0.108882 
+0.395337 0.301848 0.068427 0.015076 0.594007 0.582457 0.069673 0.044261 0.366317 4.145067 
+0.536518 6.326067 2.145078 0.282959 0.013266 3.234294 1.807177 0.296636 0.697264 0.159069 0.137500 
+1.124035 0.484133 0.371004 0.025548 0.893680 1.672569 0.173735 0.139538 0.442472 4.273607 6.312358 0.656604 
+0.253701 0.052722 0.089525 0.017416 1.105251 0.035855 0.018811 0.089586 0.682139 1.112727 2.592692 0.023918 1.798853 
+1.177651 0.332533 0.161787 0.394456 0.075382 0.624294 0.419409 0.196961 0.508851 0.078281 0.249060 0.390322 0.099849 0.094464 
+4.727182 0.858151 4.008358 1.240275 2.784478 1.223828 0.611973 1.739990 0.990012 0.064105 0.182287 0.748683 0.346960 0.361819 1.338132 
+2.139501 0.578987 2.000679 0.425860 1.143480 1.080136 0.604545 0.129836 0.584262 1.033739 0.302936 1.136863 2.020366 0.165001 0.571468 6.472279 
+0.180717 0.593607 0.045376 0.029890 0.670128 0.236199 0.077852 0.268491 0.597054 0.111660 0.619632 0.049906 0.696175 2.457121 0.095131 0.248862 0.140825 
+0.218959 0.314440 0.612025 0.135107 1.165532 0.257336 0.120037 0.054679 5.306834 0.232523 0.299648 0.131932 0.481306 7.803902 0.089613 0.400547 0.245841 3.151815 
+2.547870 0.170887 0.083688 0.037967 1.959291 0.210332 0.245034 0.076701 0.119013 10.649107 1.702745 0.185202 1.898718 0.654683 0.296501 0.098369 2.188158 0.189510 0.249313 
+
+0.069161169904116707 0.056884674049556723 0.035833476434349185 0.0479407202638895 0.022133798888638229 0.048263034257822017 0.072011405431553377 0.065918753416186013 0.02601579274034517 0.043181461066983624 0.098454003966423453 0.057435220134256809 0.021731264148762204 0.035697362115156471 0.06389942972842233 0.083537350487497455 0.053669110046364731 0.012227168092626202 0.026166076866009188 0.059838727961040609
+
+//
+ A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V
+Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
+
+	Symmetrical part of the rate matrix and aa frequencies,
+estimated from 3905 globular protein amino acid sequences forming 182
+protein families.
+	The first part above indicates the symmetric 'exchangeability'
+parameters, where s_ij = s_ji.  The s_ij above are not scaled, but the
+PAML package will perform this scaling.
+	The second part gives the amino acid frequencies (pi_i)
+estimated from the 3905 sequences.  The net replacement rate from i to
+j is Q_ij = s_ij*pi_j.
+
+
+Citation:
+
+Le, S. Q., and O. Gascuel. 2008. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25:1307-1320.