Update iqtree2 Dockerfile - fix broken link

[Kincekara]

• fix broken iqtree2 link that prevents deploy

Pull Request (PR) checklist:

• [x] Include a description of what is in this pull request in this message.
• [x] The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
• [x] Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
  • [ ] (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• [x] Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • [ ] If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• [x] Dockerfile includes the recommended LABELS
• [x] Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• [x] Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[jessicarowell]

Looks like build to test succeeded!

#10 [test 2/2] RUN iqtree2 -s /iqtree-2.3.4-Linux-intel/example.phy --rate
#10 0.055 IQ-TREE multicore version 2.3.4 COVID-edition for Linux x86 64-bit built Apr 26 2024
#10 0.055 Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung, Olga Chernomor,
#10 0.055 Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan, Thomas Wong
#10 0.055 
#10 0.055 Host:    buildkitsandbox (AVX2, FMA3, 15 GB RAM)
#10 0.055 Command: iqtree2 -s /iqtree-2.3.4-Linux-intel/example.phy --rate
#10 0.055 Seed:    663463 (Using SPRNG - Scalable Parallel Random Number Generator)
#10 0.058 Time:    Wed May 29 15:26:24 2024
#10 0.058 Kernel:  AVX+FMA - 1 threads (4 CPU cores detected)
#10 0.058 
#10 0.058 HINT: Use -nt option to specify number of threads because your CPU has 4 cores!
#10 0.058 HINT: -nt AUTO will automatically determine the best number of threads to use.
#10 0.058 
#10 0.059 Reading alignment file /iqtree-2.3.4-Linux-intel/example.phy ... Phylip format detected
#10 0.060 Alignment most likely contains DNA/RNA sequences
#10 0.062 Alignment has 17 sequences with 1998 columns, 1152 distinct patterns
#10 0.062 1009 parsimony-informative, 303 singleton sites, 686 constant sites
#10 0.063            Gap/Ambiguity  Composition  p-value
#10 0.063 Analyzing sequences: done in 5.79357e-05 secs using 100.1% CPU
#10 0.063    1  LngfishAu    0.15%    passed      6.20%
#10 0.063    2  LngfishSA    0.00%    failed      0.62%
#10 0.063    3  LngfishAf    0.05%    failed      1.60%
#10 0.063    4  Frog         0.05%    passed     58.01%
#10 0.063    5  Turtle       0.15%    passed     44.25%
#10 0.063    6  Sphenodon    0.10%    passed     59.78%
#10 0.063    7  Lizard       0.90%    passed     38.67%
#10 0.063    8  Crocodile    0.35%    failed      2.51%
#10 0.063    9  Bird         0.00%    failed      0.00%
#10 0.063   10  Human        0.00%    failed      0.85%
#10 0.063   11  Seal         0.00%    passed     68.93%
#10 0.063   12  Cow          0.00%    passed     59.11%
#10 0.063   13  Whale        0.00%    passed     97.83%
#10 0.063   14  Mouse        0.05%    failed      1.43%
#10 0.063   15  Rat          0.00%    passed     39.69%
#10 0.063   16  Platypus     0.00%    failed      3.46%
#10 0.063   17  Opossum      0.00%    failed      0.01%
#10 0.063 ****  TOTAL        0.11%  8 sequences failed composition chi2 test (p-value<5%; df=3)
#10 0.063 
#10 0.071 
#10 0.072 Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.001 seconds
#10 0.073 Perform fast likelihood tree search using GTR+I+G model...
#10 0.073 Estimate model parameters (epsilon = 5.000)
#10 0.235 Perform nearest neighbor interchange...
#10 0.258 Estimate model parameters (epsilon = 1.000)
#10 0.258 1. Initial log-likelihood: -21149.163
#10 0.278 Optimal log-likelihood: -21149.022
#10 0.278 Rate parameters:  A-C: 3.81260  A-G: 5.28599  A-T: 3.90758  C-G: 0.42243  C-T: 15.53651  G-T: 1.00000
#10 0.278 Base frequencies:  A: 0.355  C: 0.228  G: 0.192  T: 0.225
#10 0.278 Proportion of invariable sites: 0.157
#10 0.278 Gamma shape alpha: 0.739
#10 0.278 Parameters optimization took 1 rounds (0.020 sec)
#10 0.279 Time for fast ML tree search: 0.206 seconds
#10 0.279 
#10 0.279 NOTE: ModelFinder requires 6 MB RAM!
#10 0.279 ModelFinder will test up to 484 DNA models (sample size: 1998) ...
#10 0.279  No. Model         -LnL         df  AIC          AICc         BIC
#10 0.305   1  GTR+F         22701.477    39  45480.955    45482.548    45699.351
#10 0.349   2  GTR+F+I       21615.548    40  43311.095    43312.771    43535.091
#10 0.504   3  GTR+F+G4      21155.969    40  42391.938    42393.614    42615.934
#10 0.530   4  GTR+F+I+G4    21148.848    41  42379.697    42381.458    42609.293
#10 0.609   5  GTR+F+R2      21235.663    41  42553.325    42555.086    42782.921
#10 0.825   6  GTR+F+R3      21147.207    43  42380.415    42382.351    42621.211
#10 1.134   7  GTR+F+R4      21145.838    45  42381.677    42383.798    42633.672
#10 1.226  14  GTR+F+I+R2    21174.481    42  42432.962    42434.810    42668.158
#10 1.428  15  GTR+F+I+R3    21146.803    44  42381.607    42383.634    42628.002
#10 1.705  16  GTR+F+I+R4    21146.279    46  42384.558    42386.775    42642.154
#10 1.797  25  SYM+G4        21317.781    37  42709.562    42710.997    42916.759
#10 1.899  26  SYM+I+G4      21306.171    38  42688.342    42689.855    42901.138
#10 1.959  47  TVM+F+G4      21300.237    39  42678.474    42680.067    42896.870
#10 2.032  48  TVM+F+I+G4    21288.271    40  42656.543    42658.219    42880.539
#10 2.112  69  TVMe+G4       21422.187    36  42916.374    42917.733    43117.971
#10 2.215  70  TVMe+I+G4     21407.602    37  42889.204    42890.638    43096.400
#10 2.267  91  TIM3+F+G4     21367.926    38  42811.853    42813.366    43024.649
#10 2.324  92  TIM3+F+I+G4   21359.481    39  42796.962    42798.556    43015.359
#10 2.396 113  TIM3e+G4      21717.462    35  43504.924    43506.208    43700.920
#10 2.481 114  TIM3e+I+G4    21708.559    36  43489.119    43490.477    43690.715
#10 2.505 135  TIM2+F+G4     21159.705    38  42395.410    42396.923    42[608](https://github.com/StaPH-B/docker-builds/actions/runs/9288874436/job/25561387046#step:8:613).206
#10 2.526 136  TIM2+F+I+G4   21152.488    39  42382.976    42384.570    42601.372
#10 2.595 157  TIM2e+G4      21320.880    35  42711.761    42713.045    42907.757
#10 2.684 158  TIM2e+I+G4    21309.128    36  42690.256    42691.614    42891.852
#10 2.735 179  TIM+F+G4      21368.782    38  42813.564    42815.077    43026.360
#10 2.791 180  TIM+F+I+G4    21360.237    39  42798.474    42800.067    43016.870
#10 2.864 201  TIMe+G4       21718.131    35  43506.263    43507.547    43702.259
#10 2.949 202  TIMe+I+G4     21709.220    36  43490.441    43491.799    43692.037
#10 3.008 223  TPM3u+F+G4    21488.893    37  43051.786    43053.220    43258.982
#10 3.075 224  TPM3u+F+I+G4  21474.935    38  43025.870    43027.383    43238.666
#10 3.142 245  TPM3+G4       21847.239    34  43762.478    43763.690    43952.875
#10 3.221 246  TPM3+I+G4     21833.461    35  43736.922    43738.206    43932.919
#10 3.264 267  TPM2u+F+G4    21303.797    37  42681.595    42683.030    42888.791
#10 3.323 268  TPM2u+F+I+G4  21291.867    38  42659.735    42661.248    42872.531
#10 3.380 289  TPM2+G4       21424.733    34  42917.467    42918.679    43107.864
#10 3.458 290  TPM2+I+G4     21410.281    35  42890.562    42891.846    43086.559
#10 3.514 311  K3Pu+F+G4     21489.348    37  43052.696    43054.131    43259.892
#10 3.577 312  K3Pu+F+I+G4   21475.430    38  43026.861    43028.374    43239.657
#10 3.645 333  K3P+G4        21847.490    34  43762.981    43764.193    43953.378
#10 3.721 334  K3P+I+G4      21833.795    35  43737.591    43738.875    43933.587
#10 3.764 355  TN+F+G4       21369.048    37  42812.096    42813.531    43019.293
#10 3.811 356  TN+F+I+G4     21360.518    38  42797.036    42798.549    43009.832
#10 3.869 377  TNe+G4        21718.202    34  43504.403    43505.[616](https://github.com/StaPH-B/docker-builds/actions/runs/9288874436/job/25561387046#step:8:621)    43694.800
#10 3.934 378  TNe+I+G4      21709.280    35  43488.561    43489.845    43684.557
#10 3.979 399  HKY+F+G4      21489.737    36  43051.475    43052.833    43253.071
#10 4.031 400  HKY+F+I+G4    21475.768    37  43025.535    43026.970    43232.732
#10 4.085 421  K2P+G4        21847.675    33  43761.349    43762.492    43946.146
#10 4.149 422  K2P+I+G4      21833.949    34  43735.897    43737.110    43926.294
#10 4.175 443  F81+F+G4      22031.578    35  44133.155    44134.440    44329.152
#10 4.215 444  F81+F+I+G4    22019.576    36  44111.152    44112.510    44312.748
#10 4.242 465  JC+G4         22258.086    32  44580.172    44581.246    44759.368
#10 4.303 466  JC+I+G4       22245.553    33  44557.106    44558.249    44741.903
#10 4.303 Akaike Information Criterion:           GTR+F+I+G4
#10 4.303 Corrected Akaike Information Criterion: GTR+F+I+G4
#10 4.303 Bayesian Information Criterion:         TIM2+F+I+G4
#10 4.303 Best-fit model: TIM2+F+I+G4 chosen according to BIC
#10 4.303 
#10 4.303 All model information printed to /iqtree-2.3.4-Linux-intel/example.phy.model.gz
#10 4.303 CPU time for ModelFinder: 4.231 seconds (0h:0m:4s)
#10 4.303 Wall-clock time for ModelFinder: 4.240 seconds (0h:0m:4s)
#10 4.310 
#10 4.310 NOTE: 2 MB RAM (0 GB) is required!
#10 4.310 Estimate model parameters (epsilon = 0.100)
#10 4.310 Thoroughly optimizing +I+G parameters from 10 start values...
#10 4.380 Init pinv, alpha: 0.000, 0.738 / Estimate: 0.000, 0.483 / LogL: -21159.748
#10 4.443 Init pinv, alpha: 0.038, 0.738 / Estimate: 0.043, 0.532 / LogL: -21156.976
#10 4.507 Init pinv, alpha: 0.076, 0.738 / Estimate: 0.085, 0.592 / LogL: -21154.640
#10 4.543 Init pinv, alpha: 0.114, 0.738 / Estimate: 0.120, 0.654 / LogL: -21153.214
#10 4.553 Init pinv, alpha: 0.153, 0.738 / Estimate: 0.153, 0.726 / LogL: -21152.514
#10 4.589 Init pinv, alpha: 0.191, 0.738 / Estimate: 0.183, 0.803 / LogL: -21152.778
#10 4.675 Init pinv, alpha: 0.229, 0.738 / Estimate: 0.187, 0.817 / LogL: -21152.912
#10 4.806 Init pinv, alpha: 0.267, 0.738 / Estimate: 0.186, 0.813 / LogL: -21152.863
#10 4.956 Init pinv, alpha: 0.305, 0.738 / Estimate: 0.186, 0.813 / LogL: -21152.876
#10 5.117 Init pinv, alpha: 0.343, 0.738 / Estimate: 0.187, 0.816 / LogL: -21152.903
#10 5.117 Optimal pinv,alpha: 0.153, 0.726 / LogL: -21152.514
#10 5.117 
#10 5.117 Parameters optimization took 0.807 sec
#10 5.118 Wrote distance file to... 
#10 5.118 Computing ML distances based on estimated model parameters...
#10 5.119 Calculating distance matrix: done in 0.00109601 secs using 99.91% CPU
#10 5.119 Computing ML distances took 0.001257 sec (of wall-clock time) 0.001258 sec (of CPU time)
#10 5.120 Setting up auxiliary I and S matrices: done in 4.1008e-05 secs using 97.54% CPU
#10 5.120 Computing RapidNJ tree took 0.000190 sec (of wall-clock time) 0.000162 sec (of CPU time)
#10 5.133 Log-likelihood of RapidNJ tree: -21161.699
#10 5.133 --------------------------------------------------------------------
#10 5.133 |             INITIALIZING CANDIDATE TREE SET                      |
#10 5.133 --------------------------------------------------------------------
#10 5.133 Generating 98 parsimony trees... 0.146 second
#10 5.515 Computing log-likelihood of 98 initial trees ... 0.236 seconds
#10 5.515 Current best score: -21152.514
#10 5.515 
#10 5.515 Do NNI search on 20 best initial trees
#10 5.524 Estimate model parameters (epsilon = 0.100)
#10 5.534 BETTER TREE FOUND at iteration 1: -21152.510
#10 5.752 Iteration 10 / LogL: -21152.548 / Time: 0h:0m:5s
#10 6.054 Iteration 20 / LogL: -21152.548 / Time: 0h:0m:5s
#10 6.055 Finish initializing candidate tree set (2)
#10 6.055 Current best tree score: -21152.510 / CPU time: 0.921
#10 6.055 Number of iterations: 20
#10 6.055 --------------------------------------------------------------------
#10 6.055 |               OPTIMIZING CANDIDATE TREE SET                      |
#10 6.055 --------------------------------------------------------------------
#10 6.370 Iteration 30 / LogL: -21152.539 / Time: 0h:0m:6s (0h:0m:5s left)
#10 6.675 Iteration 40 / LogL: -21152.569 / Time: 0h:0m:6s (0h:0m:3s left)
#10 6.988 Iteration 50 / LogL: -21152.646 / Time: 0h:0m:6s (0h:0m:2s left)
#10 7.324 Iteration 60 / LogL: -21158.500 / Time: 0h:0m:7s (0h:0m:2s left)
#10 7.[623](https://github.com/StaPH-B/docker-builds/actions/runs/9288874436/job/25561387046#step:8:628) Iteration 70 / LogL: -21152.680 / Time: 0h:0m:7s (0h:0m:1s left)
#10 7.945 Iteration 80 / LogL: -21152.798 / Time: 0h:0m:7s (0h:0m:0s left)
#10 8.212 Iteration 90 / LogL: -21152.[624](https://github.com/StaPH-B/docker-builds/actions/runs/9288874436/job/25561387046#step:8:629) / Time: 0h:0m:8s (0h:0m:0s left)
#10 8.512 Iteration 100 / LogL: -21157.860 / Time: 0h:0m:8s (0h:0m:0s left)
#10 8.562 TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:8s
#10 8.562 
#10 8.562 --------------------------------------------------------------------
#10 8.562 |                    FINALIZING TREE SEARCH                        |
#10 8.562 --------------------------------------------------------------------
#10 8.562 Performs final model parameters optimization
#10 8.563 Estimate model parameters (epsilon = 0.010)
#10 8.563 1. Initial log-likelihood: -21152.510
#10 8.572 Optimal log-likelihood: -21152.506
#10 8.572 Rate parameters:  A-C: 5.70993  A-G: 7.80511  A-T: 5.70993  C-G: 1.00000  C-T: 23.18139  G-T: 1.00000
#10 8.572 Base frequencies:  A: 0.355  C: 0.228  G: 0.192  T: 0.225
#10 8.572 Proportion of invariable sites: 0.154
#10 8.572 Gamma shape alpha: 0.728
#10 8.573 Parameters optimization took 1 rounds (0.010 sec)
#10 8.573 BEST SCORE FOUND : -21152.506
#10 8.581 Empirical proportions for each category: 0.142 0.266 0.182 0.195 0.216
#10 8.581 Site rates printed to /iqtree-2.3.4-Linux-intel/example.phy.rate
#10 8.581 Total tree length: 4.227
#10 8.581 
#10 8.581 Total number of iterations: 102
#10 8.581 CPU time used for tree search: 3.608 sec (0h:0m:3s)
#10 8.581 Wall-clock time used for tree search: 3.429 sec (0h:0m:3s)
#10 8.581 Total CPU time used: 8.692 sec (0h:0m:8s)
#10 8.581 Total wall-clock time used: 8.518 sec (0h:0m:8s)
#10 8.583 
#10 8.583 Analysis results written to: 
#10 8.583   IQ-TREE report:                /iqtree-2.3.4-Linux-intel/example.phy.iqtree
#10 8.583   Maximum-likelihood tree:       /iqtree-2.3.4-Linux-intel/example.phy.treefile
#10 8.583   Likelihood distances:          /iqtree-2.3.4-Linux-intel/example.phy.mldist
#10 8.583   Site-specific rates:           /iqtree-2.3.4-Linux-intel/example.phy.rate
#10 8.583   Screen log file:               /iqtree-2.3.4-Linux-intel/example.phy.log
#10 8.583 
#10 8.583 Date and Time: Wed May 29 15:26:33 2024
#10 DONE 8.6s