issue on running example container

[skr3178]

$ docker pull biocontainers/blast:2.2.31

docker run biocontainers/blast:2.2.31 blastp -help

C:\WINDOWS\system32> docker run biocontainers/blast:2.2.31 blastp -help USAGE blastp [-h] [-help] [-import_search_strategy filename] [-export_search_strategy filename] [-task task_name] [-db database_name] [-dbsize num_letters] [-gilist filename] [-seqidlist filename] [-negative_gilist filename] [-entrez_query entrez_query] [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm] [-subject subject_input_file] [-subject_loc range] [-query input_file] [-out output_file] [-evalue evalue] [-word_size int_value] [-gapopen open_penalty] [-gapextend extend_penalty] [-qcov_hsp_perc float_value] [-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_value] [-sum_stats bool_value] [-seg SEG_options] [-soft_masking soft_masking] [-matrix matrix_name] [-threshold float_value] [-culling_limit int_value] [-best_hit_overhang float_value] [-best_hit_score_edge float_value] [-window_size int_value] [-lcase_masking] [-query_loc range] [-parse_deflines] [-outfmt format] [-show_gis] [-num_descriptions int_value] [-num_alignments int_value] [-line_length line_length] [-html] [-max_target_seqs num_sequences] [-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo] [-use_sw_tback] [-version]

DESCRIPTION Protein-Protein BLAST 2.2.31+

OPTIONAL ARGUMENTS -h Print USAGE and DESCRIPTION; ignore all other parameters -help Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters -version Print version number; ignore other arguments

*** Input query options -query Input file name Default = `-' -query_loc Location on the query sequence in 1-based offsets (Format: start-stop)

** General search options -task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short' > Task to execute Default = blastp' -db BLAST database name Incompatible with: subject, subject_loc -out Output file name Default = -' -evalue Expectation value (E) threshold for saving hits Default = 10' -word_size <Integer, >=2> Word size for wordfinder algorithm -gapopen Cost to open a gap -gapextend Cost to extend a gap -matrix Scoring matrix name (normally BLOSUM62) -threshold <Real, >=0> Minimum word score such that the word is added to the BLAST lookup table -comp_based_stats Use composition-based statistics: D or d: default (equivalent to 2 ) 0 or F or f: No composition-based statistics 1: Composition-based statistics as in NAR 29:2994-3005, 2001 2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally Default = 2'

*** BLAST-2-Sequences options -subject Subject sequence(s) to search

• Incompatible with: db, gilist, seqidlist, negative_gilist, db_soft_mask, db_hard_mask -subject_loc Location on the subject sequence in 1-based offsets (Format: start-stop)
• Incompatible with: db, gilist, seqidlist, negative_gilist, db_soft_mask, db_hard_mask, remote

*** Formatting options -outfmt alignment view options: 0 = pairwise, 1 = query-anchored showing identities, 2 = query-anchored no identities, 3 = flat query-anchored, show identities, 4 = flat query-anchored, no identities, 5 = XML Blast output, 6 = tabular, 7 = tabular with comment lines, 8 = Text ASN.1, 9 = Binary ASN.1, 10 = Comma-separated values, 11 = BLAST archive format (ASN.1), 12 = JSON Seqalign output, 13 = JSON Blast output, 14 = XML2 Blast output

Options 6, 7, and 10 can be additionally configured to produce a custom format specified by space delimited format specifiers. The supported format specifiers are: qseqid means Query Seq-id qgi means Query GI qacc means Query accesion qaccver means Query accesion.version qlen means Query sequence length sseqid means Subject Seq-id sallseqid means All subject Seq-id(s), separated by a ';' sgi means Subject GI sallgi means All subject GIs sacc means Subject accession saccver means Subject accession.version sallacc means All subject accessions slen means Subject sequence length qstart means Start of alignment in query qend means End of alignment in query sstart means Start of alignment in subject send means End of alignment in subject qseq means Aligned part of query sequence sseq means Aligned part of subject sequence evalue means Expect value bitscore means Bit score score means Raw score length means Alignment length pident means Percentage of identical matches nident means Number of identical matches mismatch means Number of mismatches positive means Number of positive-scoring matches gapopen means Number of gap openings gaps means Total number of gaps ppos means Percentage of positive-scoring matches frames means Query and subject frames separated by a '/' qframe means Query frame sframe means Subject frame btop means Blast traceback operations (BTOP) staxids means unique Subject Taxonomy ID(s), separated by a ';' (in numerical order) sscinames means unique Subject Scientific Name(s), separated by a ';' scomnames means unique Subject Common Name(s), separated by a ';' sblastnames means unique Subject Blast Name(s), separated by a ';' (in alphabetical order) sskingdoms means unique Subject Super Kingdom(s), separated by a ';' (in alphabetical order) stitle means Subject Title salltitles means All Subject Title(s), separated by a '<>' sstrand means Subject Strand qcovs means Query Coverage Per Subject qcovhsp means Query Coverage Per HSP When not provided, the default value is: 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore', which is equivalent to the keyword 'std' Default = 0' -show_gis Show NCBI GIs in deflines? -num_descriptions <Integer, >=0> Number of database sequences to show one-line descriptions for Not applicable for outfmt > 4 Default = 500'

• Incompatible with: max_target_seqs -num_alignments <Integer, >=0> Number of database sequences to show alignments for Default = 250' * Incompatible with: max_target_seqs -line_length <Integer, >=1> Line length for formatting alignments Not applicable for outfmt > 4 Default = 60' -html Produce HTML output?

*** Query filtering options -seg Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable) Default = no' -soft_masking Apply filtering locations as soft masks Default = false' -lcase_masking Use lower case filtering in query and subject sequence(s)?

*** Restrict search or results -gilist Restrict search of database to list of GI's

• Incompatible with: negative_gilist, seqidlist, remote, subject, subject_loc -seqidlist Restrict search of database to list of SeqId's
• Incompatible with: gilist, negative_gilist, remote, subject, subject_loc -negative_gilist Restrict search of database to everything except the listed GIs
• Incompatible with: gilist, seqidlist, remote, subject, subject_loc -entrez_query Restrict search with the given Entrez query
• Requires: remote -db_soft_mask Filtering algorithm ID to apply to the BLAST database as soft masking
• Incompatible with: db_hard_mask, subject, subject_loc -db_hard_mask Filtering algorithm ID to apply to the BLAST database as hard masking
• Incompatible with: db_soft_mask, subject, subject_loc -qcov_hsp_perc <Real, 0..100> Percent query coverage per hsp -max_hsps <Integer, >=1> Set maximum number of HSPs per subject sequence to save for each query -culling_limit <Integer, >=0> If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit
• Incompatible with: best_hit_overhang, best_hit_score_edge -best_hit_overhang <Real, (>0 and <0.5)> Best Hit algorithm overhang value (recommended value: 0.1)
• Incompatible with: culling_limit -best_hit_score_edge <Real, (>0 and <0.5)> Best Hit algorithm score edge value (recommended value: 0.1)
• Incompatible with: culling_limit -max_target_seqs <Integer, >=1> Maximum number of aligned sequences to keep Not applicable for outfmt <= 4 Default = `500'
• Incompatible with: num_descriptions, num_alignments

*** Statistical options -dbsize Effective length of the database -searchsp <Int8, >=0> Effective length of the search space -sum_stats Use sum statistics

*** Search strategy options -import_search_strategy Search strategy to use

• Incompatible with: export_search_strategy -export_search_strategy File name to record the search strategy used
• Incompatible with: import_search_strategy

*** Extension options -xdrop_ungap X-dropoff value (in bits) for ungapped extensions -xdrop_gap X-dropoff value (in bits) for preliminary gapped extensions -xdrop_gap_final X-dropoff value (in bits) for final gapped alignment -window_size <Integer, >=0> Multiple hits window size, use 0 to specify 1-hit algorithm -ungapped Perform ungapped alignment only?

*** Miscellaneous options -parse_deflines Should the query and subject defline(s) be parsed? -num_threads <Integer, >=1> Number of threads (CPUs) to use in the BLAST search Default = `1'

• Incompatible with: remote -remote Execute search remotely?
• Incompatible with: gilist, seqidlist, negative_gilist, subject_loc, num_threads -use_sw_tback Compute locally optimal Smith-Waterman alignments?

[osallou]

What is the issue here?

You run the help command and get it

[bgruening]

I tested the container and it works for me and the binary prints a help. Please reopen if its still a problem.