biocontainers/edu

BioContainers Documentation.

edu's Issues

Singularity

Other than a brief mention on the very first page. There is nothing mentioned on singularity containers.

How do they fit in the CI work flow?
Why does some software have them in the registry but others don't

Look at the tools on the github it looks like the docker images are nightly built as singualrity images and hosted at:
https://depot.galaxyproject.org/singularity/.
Is every image on this directory generated this way?

certificate problem on http://biocontainers-edu.biocontainers.pro

There is an issue with displaying the webpage hosted by readthedocs: the HTTPS certificate comes from readthedocs, so it is not valid in biocontainers.pro (see below). However, the https link is referenced by Google, so users can try to access it on https :(

New documentation using readthedocs

Dear @prvst @bebatut @tfursten @dbready @andreas-wilm @Maryom @bgruening @jduckles @delirehberi @cgirardot @starpharm @mr-c :

First of all thanks for your contribution to BioContainers Documentation. We recently move the documentation from Jekyll to Readthedocs which makes the documentation cleaner and easy to deploy (see the results here - https://biocontainers-edu.readthedocs.io/en/latest/ - ). You can contribute now by adding new sessions in the read_docs branch and the docs folder.

Some topics still are missing in the documentation if you would like to contribute:

• BioContainers and CWL.
• BioContainers and python notebooks.

issue on running example container

$ 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 <File_In>
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 <String> BLAST database name * Incompatible with: subject, subject_loc -out <File_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 <Integer> Cost to open a gap -gapextend <Integer> Cost to extend a gap -matrix <String> 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 <String> 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 <File_In>
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 <Boolean> 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 <File_In>
Search strategy to use
* Incompatible with: export_search_strategy
-export_search_strategy <File_Out>
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?

How to use the singularity links?

It would be great to have a simple example of how to use the singularity images. I am puzzled about what to do with the https link.

I think something like this example could be helpful to many users.

wget  https://depot.galaxyproject.org/singularity/multiqc:1.9--pyh9f0ad1d_0
chmod +x multiqc\:1.9--pyh9f0ad1d_0
./multiqc\:1.9--pyh9f0ad1d_0

(this doesn't work for me, so as a first step, would be good to see if I'm doing it wrong)