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raxml: add python requirement #2707

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Dec 2, 2019
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raxml: add python requirement #2707

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0a8b825
raxml: add python requirement
bernt-matthias Nov 30, 2019
12fd62c
bump
bernt-matthias Nov 30, 2019
164f79f
raxml: add ftype attribute to output nodes
bernt-matthias Dec 1, 2019
5f148a7
raxml: remove filenames from newick output
bernt-matthias Dec 1, 2019
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3 changes: 2 additions & 1 deletion tools/raxml/raxml.xml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4">
<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4+galaxy1">
<description>- Maximum Likelihood based inference of large phylogenetic trees</description>
<requirements>
<requirement type="package" version="8.2.4">raxml</requirement>
<requirement type="package" version="3.6">python</requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
## binary is hard-coded to the pthreads enabled raxml executable if threads > 1
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97 changes: 10 additions & 87 deletions tools/raxml/test-data/RAxML_parsimonyTree.galaxy.multi
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@@ -1,87 +1,10 @@


Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"



This is RAxML version 8.2.4 released by Alexandros Stamatakis on October 02 2015.

With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)

Alignment has 34 distinct alignment patterns

Proportion of gaps and completely undetermined characters in this alignment: 0.00%

RAxML rapid hill-climbing mode

Using 1 distinct models/data partitions with joint branch length optimization


Executing 5 inferences on the original alignment using 5 distinct randomized MP trees

All free model parameters will be estimated by RAxML
ML estimate of 25 per site rate categories

Likelihood of final tree will be evaluated and optimized under GAMMA

GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units

Partition: 0
Alignment Patterns: 34
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR




RAxML was called as follows:

raxmlHPC -s /tmp/tmpS1corm/files/000/dataset_7.dat -n galaxy -m GTRCAT -N 5 -f d -p 1234567890


Partition: 0 with name: No Name Provided
Base frequencies: 0.325 0.288 0.168 0.218

Inference[0]: Time 0.216205 CAT-based likelihood -318.296661, best rearrangement setting 5
alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 156.924095 909.973305 698.798586 49.826281 1854.008494 1.000000
Inference[1]: Time 0.156515 CAT-based likelihood -320.216706, best rearrangement setting 5
alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 984.611489 1694.475132 1327.909793 133.166551 5344.045057 1.000000
Inference[2]: Time 0.168518 CAT-based likelihood -317.720618, best rearrangement setting 5
alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 467.628294 1755.581565 1080.117186 84.613232 3889.913949 1.000000
Inference[3]: Time 0.151635 CAT-based likelihood -320.856852, best rearrangement setting 5
alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 951.225250 1754.836760 1010.717630 104.250644 4976.305821 1.000000
Inference[4]: Time 0.148819 CAT-based likelihood -320.068842, best rearrangement setting 5
alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 1216.938988 2115.384600 1728.203983 157.161613 6782.996281 1.000000


Conducting final model optimizations on all 5 trees under GAMMA-based models ....

Inference[0] final GAMMA-based Likelihood: -378.273666 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.0
Inference[1] final GAMMA-based Likelihood: -378.202304 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.1
Inference[2] final GAMMA-based Likelihood: -377.272824 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.2
Inference[3] final GAMMA-based Likelihood: -377.004321 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.3
Inference[4] final GAMMA-based Likelihood: -378.202304 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.4


Starting final GAMMA-based thorough Optimization on tree 3 likelihood -377.004321 ....

Final GAMMA-based Score of best tree -377.004321

Program execution info written to /tmp/tmpS1corm/job_working_directory/000/4/RAxML_info.galaxy
Best-scoring ML tree written to: /tmp/tmpS1corm/job_working_directory/000/4/RAxML_bestTree.galaxy

Overall execution time: 0.917038 secs or 0.000255 hours or 0.000011 days


OM: CLI options DEBUG START:
<Values at 0x7f8e104919e0: {'bootseed': None, 'groupingfile': None, 'posterior_bootstopping_analysis': None, 'print_branch_lengths': None, 'starting_tree': None, 'model_opt_precision': None, 'weightfile': None, 'use_median_approximation': None, 'majority_rule_consensus': None, 'excludefile': None, 'save_memory_gappy_alignments': None, 'binary': 'raxmlHPC', 'numofcats': None, 'multistate_sub_model': None, 'multiple_model': None, 'search_complete_random_tree': None, 'source': '/tmp/tmpS1corm/files/000/dataset_7.dat', 'outgroup_name': None, 'estimate_individual_branch_lengths': None, 'ml_search_convergence': None, 'file_multiple_trees': None, 'rapid_bootstrap_random_seed': None, 'random_seed': 1234567890, 'disable_undetermined_seq_check': None, 'save_memory_cat_model': None, 'enable_evol_heuristics': None, 'aa_empirical_freq': None, 'threads': 1, 'external_protein_model': None, 'search_algorithm': 'd', 'constraint_file': None, 'secondary_structure_model': None, 'number_of_runs': 5, 'name': None, 'initial_rearrangement_setting': None, 'secondary_structure_file': None, 'model_type': 'nucleotide', 'aa_search_matrix': None, 'disable_rate_heterogeneity': None, 'base_model': 'GTRCAT', 'parsimony_starting_tree_only': None, 'number_of_runs_bootstop': None, 'sliding_window_size': None, 'bin_model_parameter_file': None}>
OM: CLI options DEBUG END
RAxML_parsimonyTree.galaxy.RUN.0
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Is it expected that the test data output changed so much ? Could these changes be due to galaxyproject/galaxy#9052 as well ?

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@bernt-matthias bernt-matthias Dec 1, 2019 •
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this output is a (extended) newick format. It seems that originally the content of the log file was used for this output.

I just added the ftype="nhx" attribute to the test outputs .. but I guess this won't help anyway since nhx has no sniffer (yet).

Also in my opinion the output is wrong since the names between the trees are not allowed. Question is is downstream tools silently accept this or if we should change it (it comes from the Galaxy tool specific py script)

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I'd be in favor of adhering to the correct format. 5f148a7 does this, correct ?

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To the best of my knowledge, yes.

(Whale,((((Mouse,Chicken),Human),Rat),((Frog,(Carp,Loach)),Seal)),Cow);
RAxML_parsimonyTree.galaxy.RUN.1
((Seal,(Chicken,((Rat,Human),Mouse))),((Frog,(Carp,Loach)),Whale),Cow);
RAxML_parsimonyTree.galaxy.RUN.2
((Seal,((Loach,Carp),Frog)),((((Rat,Mouse),Chicken),Human),Whale),Cow);
RAxML_parsimonyTree.galaxy.RUN.3
((Whale,(((Rat,Human),(Seal,Frog)),(Chicken,Mouse))),(Carp,Loach),Cow);
RAxML_parsimonyTree.galaxy.RUN.4
((Whale,(Frog,(Carp,Loach))),(((Rat,(Mouse,Human)),Chicken),Seal),Cow);