* [gentoo-commits] proj/sci:master commit in: sci-biology/trf-bin/, sci-biology/trf-bin/files/
@ 2017-01-31 16:47 Martin Mokrejs
0 siblings, 0 replies; only message in thread
From: Martin Mokrejs @ 2017-01-31 16:47 UTC (permalink / raw
To: gentoo-commits
commit: a2df729d9eae2e016883572c2fbfe941184f421d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 31 16:44:12 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 31 16:44:12 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a2df729d
sci-biology/trf-bin: renamed to reflect it is an upstream's binary
A lot of fixes in the ebuild as well:
- install snapshot copies of HTML docs to prevent checksum errors
- properly set MY_PV version number
- fix install location
- distinguish between 32 and 64bit binaries
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/trf-bin/files/trf.definitions.txt | 159 +++++++++++++++++
sci-biology/trf-bin/files/trf.txt | 176 +++++++++++++++++++
sci-biology/trf-bin/files/trf.whatsnew.txt | 243 ++++++++++++++++++++++++++
sci-biology/trf-bin/metadata.xml | 8 +
sci-biology/trf-bin/trf-bin-4.09.ebuild | 53 ++++++
5 files changed, 639 insertions(+)
diff --git a/sci-biology/trf-bin/files/trf.definitions.txt b/sci-biology/trf-bin/files/trf.definitions.txt
new file mode 100644
index 0000000..ddedf76
--- /dev/null
+++ b/sci-biology/trf-bin/files/trf.definitions.txt
@@ -0,0 +1,159 @@
+ [1][trflogo.png]
+
+
+
+FASTA Format:
+
+ The FASTA format is a plain text format which looks something like
+ this:
+
+ >myseq
+ AGTCGTCGCT AGCTAGCTAG CATCGAGTCT TTTCGATCGA GGACTAGACT TCTAGCTAGC
+ TAGCATAGCA TACGAGCATA TCGGTCATGA GACTGATTGG GCTTTAGCTA GCTAGCATAG
+ CATACGAGCA TATCGGTAGA CTGATTGGGT TTAGGTTACC
+
+ The first line starts with a greater than sign ">" and contains a name
+ or other identifier for the sequence. This is the sequence header and
+ must be in a single line. The remaining lines contain the sequence
+ data. The sequence can be in upper or lower case letters. Anything
+ other than letters (numbers for example) is ignored. Multiple sequences
+ can be present in the same file as long as each sequence has its own
+ header.
+
+Table Explanation:
+
+ The summary table includes the following information:
+ 1. Indices of the repeat relative to the start of the sequence.
+ 2. Period size of the repeat.
+ 3. Number of copies aligned with the consensus pattern.
+ 4. Size of consensus pattern (may differ slightly from the period
+ size).
+ 5. Percent of matches between adjacent copies overall.
+ 6. Percent of indels between adjacent copies overall.
+ 7. Alignment score.
+ 8. Percent composition for each of the four nucleotides.
+ 9. Entropy measure based on percent composition.
+
+ If the output contains more than 120 repeats, multiple linked tables
+ are produced. The links to the other tables appear at the top and
+ bottom of each table.
+
+ Note: If you save multiple linked summary table files, use the default
+ names supplied by your browser to preserve the automatic linking.
+
+Alignment Explanation:
+
+ The alignment is presented as follows:
+ 1. In each pair of lines, the actual sequence is on the top and a
+ consensus sequence for all the copies is on the bottom.
+ 2. Each pair of lines is one period except for very small patterns.
+ 3. The 10 sequence characters before and after a repeat are shown.
+ 4. Symbol * indicates a mismatch.
+ 5. Symbol - indicates an insertion or deletion.
+ 6. Statistics refers to the matches, mismatches and indels overall
+ between adjacent copies in the sequence, not between the sequence
+ and the consensus pattern.
+ 7. Distances between matching characters at corresponding positions
+ are listed as distance, number at that distance, percentage of all
+ matches.
+ 8. ACGTcount is percentage of each nucleotide in the repeat sequence.
+ 9. Consensus sequence is shown by itself.
+ 10. If chosen as an option, 500 characters of flanking sequence on each
+ side of the repeat are shown.
+
+ Note: If you save the alignment file, use the default name supplied by
+ your browser to preserve the automatic cross-referencing with the
+ summary table.
+
+Program Parameters:
+
+ Input to the program consists of a sequence file and the following
+ parameters:
+ 1. Alignment Parameters. Weights for match, mismatch and indels. These
+ parameters are for Smith-Waterman style local alignment using
+ wraparound dynamic programming. Lower weights allow alignments with
+ more mismatches and indels. Match weight is +2 in all options here.
+ Mismatch and indel weights (interpreted as negative numbers) are
+ either 3, 5, or 7. A 3 is more permissive and a 7 less permissive
+ of these types of alignments choices.
+ 2. Minimum Alignment Score. The alignment score must meet or exceed
+ this value for the repeat to be reported.
+ 3. Maximum Period Size. The period size must be no larger than this
+ value for the repeat to be reported. Period size is the programs
+ best guess at the pattern size of the tandem repeat. The program
+ will find all repeats with period size between 1 and 2000.
+ 4. Maximum TR array size. Specifies the longest TR array (the complete
+ repeating sequence) expected to be found in the input, in millions
+ of base pairs. Some sequences have very long TR arrays, such as
+ chromosome 18 in HG38 which has an array measuring over 5.3 million
+ base pairs.
+ 5. Detection Parameters. Matching probability Pm and indel probability
+ Pi. Pm = .80 and Pi = .10 by default and cannot be modified in this
+ version of the program.
+
+Options:
+
+ 1. Flanking sequence. Flanking sequence consists of the 500
+ nucleotides on each side of a repeat. Flanking sequence is recorded
+ in the alignment file. This may be useful for PCR primer
+ determination.
+ 2. Masked Sequence File. The masked sequence file is a [2]FASTA format
+ file containing a copy of the sequence with every character that
+ occurred in a tandem repeat changed to the letter 'N'. The word
+ "masked" is added to the sequence description line just after the
+ '>' character.
+ 3. Data File. The data file is a text file which contains the same
+ information, in the same order, as the repeat [3]table file, plus
+ consensus and repeat sequences. This file contains no labeling and
+ is suitable for additional processing, for example with a perl
+ script, outside of the program.
+
+
+
+ [4][USEMAP:buttonarrow.png] [5]Home
+
+ [6][USEMAP:buttonarrow.png] [7]What's New
+
+ [8][USEMAP:buttonarrow.png] [9]Submit Page
+
+ [10][USEMAP:buttonarrow.png] [11]Downloads
+
+
+
+ __________________________________________________________________
+
+ [12][bu.gif] Last revised February 22, 2016
+ Send any questions or comments to:
+ [13]Yozen Hernandez
+
+References
+
+ 1. http://tandem.bu.edu/trf/trf.html
+ 2. http://tandem.bu.edu/trf/trf.definitions.html#fasta
+ 3. http://tandem.bu.edu/trf/trf.definitions.html#table
+ 4. LYNXIMGMAP:http://tandem.bu.edu/trf/trf.definitions.html#FPMap0
+ 5. http://tandem.bu.edu/trf/trf.html
+ 6. LYNXIMGMAP:http://tandem.bu.edu/trf/trf.definitions.html#FPMap3
+ 7. http://tandem.bu.edu/trf/trf.whatnew.html
+ 8. LYNXIMGMAP:http://tandem.bu.edu/trf/trf.definitions.html#FPMap1
+ 9. http://tandem.bu.edu/trf/trf.submit.options.html
+ 10. LYNXIMGMAP:http://tandem.bu.edu/trf/trf.definitions.html#FPMap2
+ 11. http://tandem.bu.edu/trf/trf.download.html
+ 12. http://www.bu.edu/
+ 13. javascript:spamGuard('yhernand','bu.edu')
+
+[USEMAP]
+http://tandem.bu.edu/trf/trf.definitions.html#FPMap2
+ 1. http://tandem.bu.edu/trf/trf.download.html
+
+[USEMAP]
+http://tandem.bu.edu/trf/trf.definitions.html#FPMap1
+ 1. http://tandem.bu.edu/trf/trf.submit.options.html
+
+[USEMAP]
+http://tandem.bu.edu/trf/trf.definitions.html#FPMap3
+ 1. http://tandem.bu.edu/trf/trf.whatnew.html
+
+[USEMAP]
+http://tandem.bu.edu/trf/trf.definitions.html#FPMap0
+ 1. http://tandem.bu.edu/trf/trf.html
diff --git a/sci-biology/trf-bin/files/trf.txt b/sci-biology/trf-bin/files/trf.txt
new file mode 100644
index 0000000..f75ec5f
--- /dev/null
+++ b/sci-biology/trf-bin/files/trf.txt
@@ -0,0 +1,176 @@
+ [1][trflogo.png]
+
+
+Using Command Line Version of Tandem Repeats Finder
+
+ Once the program is installed you can run it with no parameters to
+ obtain information on proper usage syntax.
+
+ If you installed the program as trf then by typing trf at the command
+ line you will see the following output:
+
+Please use: trf File Match Mismatch Delta PM PI Minscore MaxPeriod [options]
+
+Where: (all weights, penalties, and scores are positive)
+ File = sequences input file
+ Match = matching weight
+ Mismatch = mismatching penalty
+ Delta = indel penalty
+ PM = match probability (whole number)
+ PI = indel probability (whole number)
+ Minscore = minimum alignment score to report
+ MaxPeriod = maximum period size to report
+ [options] = one or more of the following:
+ -m masked sequence file
+ -f flanking sequence
+ -d data file
+ -h suppress html output
+ -r no redundancy elimination
+ -l <n> maximum TR length expected (in millions) (eg, -l 3 or -l=3 for
+ 3 million)
+
+Note the sequence file should be in FASTA format:
+
+>Name of sequence
+aggaaacctgccatggcctcctggtgagctgtcctcatccactgctcgctgcctctccag
+atactctgacccatggatcccctgggtgcagccaagccacaatggccatggcgccgctgt
+actcccacccgccccaccctcctgatcctgctatggacatggcctttccacatccctgtg
+
+
+ The program accepts a minimum of eight parameters. Options can be
+ specified to generate additional files.
+
+ The following is a more detailed description of the parameters:
+ * File: The sequence file to be analyzed in FASTA format( [2]see for
+ details). Multiple sequence in the same file are allowed.
+ * Match, Mismatch, and Delta: Weights for match, mismatch and indels.
+ These parameters are for Smith-Waterman style local alignment using
+ wraparound dynamic programming. Lower weights allow alignments with
+ more mismatches and indels. A match weight of 2 has proven
+ effective with mismatch and indel penalties in the range of 3 to 7.
+ Mismatch and indel weights are interpreted as negative numbers. A 3
+ is more permissive and a 7 less permissive. The recomended values
+ for Match Mismatch and Delta are 2, 7, and 7 respectively.
+ * PM and PI: Probabilistic data is available for PM values of 80 and
+ 75 and PI values of 10 and 20. The best performance can be achieved
+ with values of PM=80 and PI=10. Values of PM=75 and PI=20 give
+ results which are very similar, but often require as much as ten
+ times the processing time when compared with values of PM=80 and
+ PI=10.
+ * Minscore: The alignment of a tandem repeat must meet or exceed this
+ alignment score to be reported. For example, if we set the matching
+ weight to 2 and the minimun score to 50, assuming perfect
+ alignment, we will need to align at least 25 characters to meet the
+ minimum score (for example 5 copies with a period of size 5).
+ * Maxperiod: Period size is the program's best guess at the pattern
+ size of the tandem repeat. The program will find all repeats with
+ period size between 1 and 2000, but the output can be limited to a
+ smaller range.
+ * -m: This is an optional parameter and when present instructs the
+ program to generate a masked sequence file. The masked sequence
+ file is a FASTA format file containing a copy of the sequence with
+ every location that occurred in a tandem repeat changed to the
+ letter 'N'. The word "masked" is added to the sequence description
+ line just after the '>' character.
+ * -f: If this option is present, flanking sequence around each repeat
+ is recorded in the alignment file. This may be useful for PCR
+ primer determination. Flanking sequence consists of the 500
+ nucleotides on each side of a repeat.
+ * -d: A data file is produced if this option is present. This file is
+ a text file which contains the same information, in the same order,
+ as the summary table file, plus consensus pattern and repeat
+ sequences. This file contains no labeling and is suitable for
+ additional processing, for example with a perl script, outside of
+ the program.
+ * -h: suppress HTML output (this automatically switches -d to ON)
+ * -l <n>: Specifies that the longest TR array expected in the input
+ is at most n million bp long. The default is 2 (for 2 million).
+ Setting this option too high may result in an error message if you
+ did not have enough availablememory. We have only tested this
+ option uo to value 29.
+ * -u: Prints the help/usage message above
+ * -v: Prints the version information
+ * -ngs: More compact .dat output on multisequence files, returns 0 on
+ success. You may pipe input in with this option using - for file
+ name. Short 50 flanks are appended to .dat output. .dat output
+ actually goes to stdout instead of file. Sequence headers are
+ displayed in output as @header. Only headers containing repeats are
+ shown.
+
+ Using recommended parameters the command line will look something like:
+ trf yoursequence.txt 2 7 7 80 10 50 500 -f -d -m
+
+ Once the program starts running it will print update messages to the
+ screen. The word "Done" will be printed when the program finishes.
+
+ For single sequence input files there will be at least two HTML format
+ output files, a repeat table file and an alignment file. If the number
+ of repeats found is greater than 120, multiple linked repeat tables are
+ produced. The links to the other tables appear at the top and the
+ bottom of each table. To view the results start by opening the first
+ repeat table file with your web browser. This file has the extension
+ ".1.html". Alignment files can be accessed from the repeat table files.
+ Alignment files end with the ".txt.html" extension.
+
+ For input files containing multiple sequences a summary page is
+ produced that links to the output of individual sequences. This file
+ has the extension "summary.html". You should start by opening this file
+ if your input had multiple sequences in the same file. Also note that
+ the output files of individual sequences will have an identifier of the
+ form ".sn." ( n an integer) embedded in the name indicating the index
+ of the sequence in the input file. The identifier is omitted for single
+ sequence input files.
+
+ For more information on the output please see [3]Table Explanation and
+ [4]Alignment Explanation.
+
+
+
+
+ [5][USEMAP:buttonarrow.png] [6]Home
+
+ [7][USEMAP:buttonarrow.png] [8]What's New
+
+ [9][USEMAP:buttonarrow.png] [10]Submit Page
+
+ [11][USEMAP:buttonarrow.png] [12]Downloads
+
+
+ __________________________________________________________________
+
+ [13][bu.gif] Last revised September 11, 2003
+ Send any questions or comments to:
+ [14]Yozen Hernandez
+
+References
+
+ 1. http://tandem.bu.edu/trf/trf.html
+ 2. http://tandem.bu.edu/trf/trf.definitions.html#fasta
+ 3. http://tandem.bu.edu/trf/trf.definitions.html#table
+ 4. http://tandem.bu.edu/trf/trf.definitions.html#alignment
+ 5. LYNXIMGMAP:http://tandem.bu.edu/trf/trf.unix.help.html#FPMap0
+ 6. http://tandem.bu.edu/trf/trf.html
+ 7. LYNXIMGMAP:http://tandem.bu.edu/trf/trf.unix.help.html#FPMap3
+ 8. http://tandem.bu.edu/trf/trf.whatnew.html
+ 9. LYNXIMGMAP:http://tandem.bu.edu/trf/trf.unix.help.html#FPMap1
+ 10. http://tandem.bu.edu/trf/trf.submit.options.html
+ 11. LYNXIMGMAP:http://tandem.bu.edu/trf/trf.unix.help.html#FPMap2
+ 12. http://tandem.bu.edu/trf/trf.download.html
+ 13. http://www.bu.edu/
+ 14. javascript:spamGuard('yhernand','bu.edu')
+
+[USEMAP]
+http://tandem.bu.edu/trf/trf.unix.help.html#FPMap2
+ 1. http://tandem.bu.edu/trf/trf.download.html
+
+[USEMAP]
+http://tandem.bu.edu/trf/trf.unix.help.html#FPMap1
+ 1. http://tandem.bu.edu/trf/trf.submit.options.html
+
+[USEMAP]
+http://tandem.bu.edu/trf/trf.unix.help.html#FPMap3
+ 1. http://tandem.bu.edu/trf/trf.whatnew.html
+
+[USEMAP]
+http://tandem.bu.edu/trf/trf.unix.help.html#FPMap0
+ 1. http://tandem.bu.edu/trf/trf.html
diff --git a/sci-biology/trf-bin/files/trf.whatsnew.txt b/sci-biology/trf-bin/files/trf.whatsnew.txt
new file mode 100644
index 0000000..8967a7d
--- /dev/null
+++ b/sci-biology/trf-bin/files/trf.whatsnew.txt
@@ -0,0 +1,243 @@
+ [1][trflogo.png]
+
+
+[newspaper.png] What's New?
+
+New For Version 4.09 (Feb 22, 2016)
+
+ [checkmark.png] new -l/-L flag allows the user to specify the length of
+ the longest expected TR array in the input sequence, in millions. The
+ default value is 2, for 2 million bp. For HG38, a value of 6 is
+ necessary.
+
+ Example usage:
+trf409.linux64.exe hg38.fasta 2 5 7 80 10 50 2000 -l 6
+
+ [checkmark.png] Setting a sufficiently high value may result in a
+ crash, very long execution time, or a sharp drop in available memory on
+ your system. We have only tested up to a value of 25.
+
+ [checkmark.png] For workloads requiring over 3GB of RAM (any value of
+ -l above 5), the 32-bit builds cannot be used.
+
+ [checkmark.png] New -v/-V flag allows you to quickly check your version
+ of TRF.
+
+ [checkmark.png] New -u/-U flag allows you to quickly display the usage
+ help text.
+
+
+New For Version 4.07b
+
+ [checkmark.png] new -ngs flag allows more compact output and piping of
+ input on linux systems, returns standard linux exit value of 0 on
+ success
+
+ [checkmark.png] temporary output is no longer written to disk
+
+ [checkmark.png] changed alignment to go further when score drops to 0
+ on first pass, more repeats are reported now
+
+ [checkmark.png] fixed bestlist structure deallocations, this
+ significantly improves run speed on multi-sequence fasta files
+
+ [checkmark.png] fixed line in alignment files "file K of N", K was off
+ by 1 before
+
+ [checkmark.png] Added check to make sure all required parameters are
+ entered from the commandline
+
+
+New For Version 4.04
+
+ [checkmark.png] Widened radius of narrowband alignment to avoid losing
+ alignment in some cases
+
+
+New For Version 4.03
+
+ [checkmark.png] Added -R switch to produce output without redundancy if
+ desired
+
+ [checkmark.png] Fixed a bug in the redundancy algorithm which sometimes
+ caused repeats to vanish
+
+ [checkmark.png] Fixed a bug when N characters being part of pattern
+ cause problems
+
+
+New For Version 4.00
+
+ [checkmark.png] Improved longer period detection and period 1 detection
+
+ [checkmark.png] Improved alignment
+
+ [checkmark.png] Added a flag to suppress HTML output (-h)
+
+ [checkmark.png] Fixed a loading sequence problem with incomplete FASTA
+ format files
+
+ [checkmark.png] Increased minimum period for larger repeats from 1.9 to
+ 1.8 (patternsize > 50)
+
+ [checkmark.png] Added Linux GUI version (GTK+)
+
+
+New For Version 3.21
+
+ [checkmark.png] Fixed Sequence Name Bug: This bug affected the parsing
+ of FASTA header on Windows versions of the program. The bug caused the
+ program to report a sequence name that had a control character appended
+ at the end and a missing parameters line in the output data file. This
+ bug surfaced as a result of version 3.20 fixes.
+
+
+New For Version 3.20
+
+ [checkmark.png] Improved Redundancy Control: We have improved the
+ program's ability to remove redundant versions of the same tandem
+ repeat. On earlier versions certain conditions could cause the
+ algorithm to leave a redundant version in the output. The new version
+ properly identifies these and removes them.
+
+ [checkmark.png] Improved End-of-Line Identification: Different
+ operating systems use different conventions for end of line (EOL)
+ character sequence in text files. We have made improvements in the
+ routines that allows TRF to read sequence text from files using various
+ EOL conventions.
+
+ [checkmark.png] Fixed Memory Overrun Bug: We have corrected a problem
+ where some large-pattern, low-scoring repeats could cause a memory
+ fault in previous versions. Thanks to Angie Hinrichs at UC Santa Cruz's
+ Genome Bioinformatics group for the bug report and the offending
+ sequence.
+
+
+
+Previous Update (Version 3.01)
+
+ [checkmark.png] Unlimited Sequence Size: We have eliminated the
+ sequence size restriction of previous versions. In this version you are
+ only limited by the memory available in your system.
+
+ [checkmark.png] Multi-Sequence Files: The program handles files
+ containing multiple sequences. Each sequence must contain its own FASTA
+ header. A summary page is produced which links to the results of
+ individual sequences.
+
+ [checkmark.png] Data File Includes Repeat Sequence: We now include
+ complete repeat sequence for each repeat record reported in the data
+ file.
+
+ [checkmark.png] Smaller Scores: The downloadable versions of the
+ program are now able to report matches with scores as low as 20. We
+ recommend caution when using this feature since very large output files
+ can be generated at this score level.
+
+ [checkmark.png] Longer Patter Sizes: The program finds repeats with
+ period size as large as 2000 base pairs.
+
+ [checkmark.png] New File Naming Convention: For input files containing
+ a single sequence the naming convention for output files has not been
+ changed. For input files containing multiple sequences a summary page
+ is produced. This file has the extension "summary.html" and contains
+ links to the repeat tables of the individual sequences. In the name of
+ each of those repeat tables and their alignment files, an additional
+ identifier ".sn." ( n an integer, for example: ".s3.") has been
+ inserted before the parameters to indicate the sequence index in the
+ input file.
+
+ [checkmark.png] Repeat Table Changes: Each table now shows the total
+ number of repeats found in the sequence and links to other tables have
+ been added at the bottom of the page.
+
+ [checkmark.png] Longer Flanking Sequence: 500 characters of flanking
+ sequence on each side of the repeat are now reported.
+
+
+ Previous Update (Version 2.02)
+
+ [checkmark.png] Multiple Repeat Tables: If the output contains more
+ than 140 repeats, multiple linked repeat tables and alignment files
+ will be produced. This will speed downloading time and overcome
+ problems with tables too big for web browsers to format.
+
+ [checkmark.png] Consensus Sequence: The program prints the consensus
+ sequence for each repeat in the alignment file, below the alignment.
+
+ [checkmark.png] Flanking Sequence: As an option, the program prints 200
+ characters of flanking sequence from each side of the repeat. This may
+ be useful for PCR primer determination. Find it in the alignment file.
+
+ [checkmark.png] Masked Sequence File: As an option, the program returns
+ a copy of the original sequence with the tandem repeats "masked" out.
+ The masked sequence file is a [2]FASTA format file with every tandem
+ repeat character changed to the letter 'N'. The word "masked" is added
+ to the sequence description line just after the '>' character.
+
+ [checkmark.png] Data File: As an option, the program returns a text
+ file containing the same data, in the same order, as the summary table
+ file, plus consensus sequences, but without any labels or formatting
+ instructions. This file is suitable for automated processing, for
+ example with a perl script.
+
+ [checkmark.png] Select Parameters: Now you can select parameters when
+ you submit a sequence, or simply use the default parameters. Visit the
+ [3]Submit Options Page for more details.
+
+ [checkmark.png] Sequence Alphabet: The program now handles sequences
+ containing letter other than A, C, G, and T.
+
+ [checkmark.png] Enhanced Alignment File: We have modified the
+ presentation of the alignment file. The output should be easier to view
+ and print.
+
+ [checkmark.png] Automatic Redundancy Removal: The program now reports
+ only the smallest period size for a repeat unless a larger period size
+ has a significantly higher score.
+
+ [checkmark.png] Windows Version Now Available: A Windows version of the
+ program is now available for download. This version of the the program
+ can be run under Windows 95/98 and Windows NT 4. Please visit our
+ [4]Download Page for more details.
+
+
+
+
+ [5][USEMAP:buttonarrow.png] [6]Home
+
+ [7][USEMAP:buttonarrow.png] [8]Submit Page
+
+ [9][USEMAP:buttonarrow.png] [10]Downloads
+ __________________________________________________________________
+
+ [11][bu.gif] Last revised February 22, 2016
+ Send any questions or comments to:
+ [12]Yozen Hernandez
+
+References
+
+ 1. http://tandem.bu.edu/trf/trf.html
+ 2. http://tandem.bu.edu/trf/trf.definitions.html#fasta
+ 3. http://tandem.bu.edu/trf/trf.submit.options.html
+ 4. http://tandem.bu.edu/trf/trf.download.html
+ 5. LYNXIMGMAP:http://tandem.bu.edu/trf/trf.whatnew.html#FPMap0
+ 6. http://tandem.bu.edu/trf/trf.html
+ 7. LYNXIMGMAP:http://tandem.bu.edu/trf/trf.whatnew.html#FPMap1
+ 8. http://tandem.bu.edu/trf/trf.submit.options.html
+ 9. LYNXIMGMAP:http://tandem.bu.edu/trf/trf.whatnew.html#FPMap2
+ 10. http://tandem.bu.edu/trf/trf.download.html
+ 11. http://www.bu.edu/
+ 12. javascript:spamGuard('yhernand','bu.edu')
+
+[USEMAP]
+http://tandem.bu.edu/trf/trf.whatnew.html#FPMap2
+ 1. http://tandem.bu.edu/trf/trf.download.html
+
+[USEMAP]
+http://tandem.bu.edu/trf/trf.whatnew.html#FPMap1
+ 1. http://tandem.bu.edu/trf/trf.submit.options.html
+
+[USEMAP]
+http://tandem.bu.edu/trf/trf.whatnew.html#FPMap0
+ 1. http://tandem.bu.edu/trf/trf.html
diff --git a/sci-biology/trf-bin/metadata.xml b/sci-biology/trf-bin/metadata.xml
new file mode 100644
index 0000000..959160f
--- /dev/null
+++ b/sci-biology/trf-bin/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/trf-bin/trf-bin-4.09.ebuild b/sci-biology/trf-bin/trf-bin-4.09.ebuild
new file mode 100644
index 0000000..11fae9c
--- /dev/null
+++ b/sci-biology/trf-bin/trf-bin-4.09.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit eutils
+
+MY_PV="${PV/.}" # drop the dot
+MY_PN="trf"
+MY_P="trf${MY_PV}"
+
+DESCRIPTION="Tandem Repeats Finder"
+HOMEPAGE="http://tandem.bu.edu/trf/trf.html"
+SRC_URI="x86? ( http://tandem.bu.edu/trf/downloads/${MY_P}.linux32 )
+ amd64? ( http://tandem.bu.edu/trf/downloads/${MY_P}.linux64 )"
+
+LICENSE="trf" # http://tandem.bu.edu/trf/trf.license.html
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+RESTRICT="mirror bindist"
+
+S="${WORKDIR}"
+
+QA_PREBUILT="opt/${MY_PN}/.*"
+
+src_unpack() {
+ if use x86; then
+ cp "${DISTDIR}/${MY_P}".linux32 "${S}/${MY_PN}" || die
+ elif use amd64; then
+ cp "${DISTDIR}/${MY_P}".linux64 "${S}/${MY_PN}" || die
+ else
+ eerror "Unsupported platform, check http://tandem.bu.edu/trf/downloads/"
+ fi
+ default
+}
+
+src_install() {
+ exeinto /opt/"${MY_PN}"/bin
+ doexe "${MY_PN}"
+ # GTK version (http://tandem.bu.edu/trf/downloads/trf400.linuxgtk.exe) has broken linking
+ #if use gtk; then
+ # doexe trf400.linuxgtk.exe
+ # make_desktop_entry /opt/${PN}/trf400.linuxgtk.exe "Tandem Repeats Finder" || die
+ #fi
+ # http://tandem.bu.edu/trf/trf.unix.help.html
+ # http://tandem.bu.edu/trf/trf.definitions.html
+ # http://tandem.bu.edu/trf/trf.whatnew.html
+ dodoc \
+ "${FILESDIR}/"trf.txt \
+ "${FILESDIR}/"trf.definitions.txt \
+ "${FILESDIR}/"trf.whatsnew.txt
+}
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2017-01-31 16:47 [gentoo-commits] proj/sci:master commit in: sci-biology/trf-bin/, sci-biology/trf-bin/files/ Martin Mokrejs
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