fix checksum for snpEff 5.0 #13062

boegel · 2021-06-05T19:23:23Z

(created using eb --new-pr)

The easyconfig added in #12898 has the correct checksum, apparently the source file was updated in place, and the code is slightly different:

$ diff -ru snpEff-5.0.old snpEff-5.0
diff -ru snpEff-5.0.old/galaxy/snpEff_download.xml snpEff-5.0/galaxy/snpEff_download.xml
--- snpEff-5.0.old/galaxy/snpEff_download.xml   2020-08-10 03:24:23.000000000 +0200
+++ snpEff-5.0/galaxy/snpEff_download.xml       2020-10-04 22:04:01.000000000 +0200
@@ -25,7 +25,7 @@

 This tool downloads a SnpEff database.

-For details about this tool, please go to http://snpEff.sourceforge.net
+For details about this tool, please go to https://pcingola.github.io/SnpEff

        </help>
 </tool>
diff -ru snpEff-5.0.old/galaxy/snpEff.xml snpEff-5.0/galaxy/snpEff.xml
--- snpEff-5.0.old/galaxy/snpEff.xml    2020-08-10 03:24:23.000000000 +0200
+++ snpEff-5.0/galaxy/snpEff.xml        2020-10-04 22:04:01.000000000 +0200
@@ -94,7 +94,7 @@

 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.

-For details about this tool, please go to http://snpEff.sourceforge.net
+For details about this tool, please go to https://pcingola.github.io/SnpEff

        </help>
 </tool>
diff -ru snpEff-5.0.old/galaxy/snpSift_annotate.xml snpEff-5.0/galaxy/snpSift_annotate.xml
--- snpEff-5.0.old/galaxy/snpSift_annotate.xml  2020-08-10 03:24:23.000000000 +0200
+++ snpEff-5.0/galaxy/snpSift_annotate.xml      2020-10-04 22:04:01.000000000 +0200
@@ -36,7 +36,7 @@

 This is typically used to annotate IDs from dbSnp.

-For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate
+For details about this tool, please go to https://pcingola.github.io/SnpEff/SnpSift.html#annotate

        </help>
 </tool>
diff -ru snpEff-5.0.old/galaxy/snpSift_caseControl.xml snpEff-5.0/galaxy/snpSift_caseControl.xml
--- snpEff-5.0.old/galaxy/snpSift_caseControl.xml       2020-08-10 03:24:23.000000000 +0200
+++ snpEff-5.0/galaxy/snpSift_caseControl.xml   2020-10-04 22:04:01.000000000 +0200
@@ -41,7 +41,7 @@

  - **CC_GEN**: p-value using Genotypic (co-dominant) model

-For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol
+For details about this tool, please go to https://pcingola.github.io/SnpEff/SnpSift.html#casecontrol

        </help>
 </tool>
diff -ru snpEff-5.0.old/galaxy/snpSift_filter.xml snpEff-5.0/galaxy/snpSift_filter.xml
--- snpEff-5.0.old/galaxy/snpSift_filter.xml    2020-08-10 03:24:23.000000000 +0200
+++ snpEff-5.0/galaxy/snpSift_filter.xml        2020-10-04 22:04:01.000000000 +0200
@@ -56,7 +56,7 @@
     * **isHom( GEN[0] ) &amp; isVariant( GEN[0] ) &amp; isRef( GEN[1] )**


-For complete details about this tool and epressions that can be used, please go to http://snpeff.sourceforge.net/SnpSift.html#filter
+For complete details about this tool and epressions that can be used, please go to https://pcingola.github.io/SnpEff/SnpSift.html#filter

        </help>
 </tool>
diff -ru snpEff-5.0.old/galaxy/snpSift_int.xml snpEff-5.0/galaxy/snpSift_int.xml
--- snpEff-5.0.old/galaxy/snpSift_int.xml       2020-08-10 03:24:23.000000000 +0200
+++ snpEff-5.0/galaxy/snpSift_int.xml   2020-10-04 22:04:01.000000000 +0200
@@ -39,7 +39,7 @@

 You can filter using intervals (BED file)

-For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals
+For details about this tool, please go to https://pcingola.github.io/SnpEff/SnpSift.html#intervals

        </help>
 </tool>
diff -ru snpEff-5.0.old/galaxy/tool-data/snpEff_genomes.loc snpEff-5.0/galaxy/tool-data/snpEff_genomes.loc
--- snpEff-5.0.old/galaxy/tool-data/snpEff_genomes.loc  2020-08-10 03:24:23.000000000 +0200
+++ snpEff-5.0/galaxy/tool-data/snpEff_genomes.loc      2020-10-04 22:04:01.000000000 +0200
@@ -13855,7 +13855,7 @@
 ASM331708v1.99          Hucho_hucho   ASM331708v1.99
 GRCh37.87       Human   GRCh37.87
 GRCh37.p13.RefSeq       Human   GRCh37.p13.RefSeq
-GRCh38.p7.RefSeq        Human   GRCh38.p7.RefSeq
+GRCh38.p13.RefSeq       Human   GRCh38.p13.RefSeq
 Humibacillus_sp_dsm_29435       Humibacillus_sp_dsm_29435   Humibacillus_sp_dsm_29435
 Hungatella_hathewayi_12489931   Hungatella_hathewayi_12489931   Hungatella_hathewayi_12489931
 Hungatella_hathewayi_dsm_13479          Hungatella_hathewayi_dsm_13479   Hungatella_hathewayi_dsm_13479
diff -ru snpEff-5.0.old/galaxy/tool-data/snpEff_genomes.loc.sample snpEff-5.0/galaxy/tool-data/snpEff_genomes.loc.sample
--- snpEff-5.0.old/galaxy/tool-data/snpEff_genomes.loc.sample   2020-08-10 03:24:23.000000000 +0200
+++ snpEff-5.0/galaxy/tool-data/snpEff_genomes.loc.sample       2020-10-04 22:04:01.000000000 +0200
@@ -13855,7 +13855,7 @@
 ASM331708v1.99          Hucho_hucho   ASM331708v1.99
 GRCh37.87       Human   GRCh37.87
 GRCh37.p13.RefSeq       Human   GRCh37.p13.RefSeq
-GRCh38.p7.RefSeq        Human   GRCh38.p7.RefSeq
+GRCh38.p13.RefSeq       Human   GRCh38.p13.RefSeq
 Humibacillus_sp_dsm_29435       Humibacillus_sp_dsm_29435   Humibacillus_sp_dsm_29435
 Hungatella_hathewayi_12489931   Hungatella_hathewayi_12489931   Hungatella_hathewayi_12489931
 Hungatella_hathewayi_dsm_13479          Hungatella_hathewayi_dsm_13479   Hungatella_hathewayi_dsm_13479
diff -ru snpEff-5.0.old/scripts/fastaSplit.pl snpEff-5.0/scripts/fastaSplit.pl
--- snpEff-5.0.old/scripts/fastaSplit.pl        2020-08-10 03:24:23.000000000 +0200
+++ snpEff-5.0/scripts/fastaSplit.pl    2020-10-04 22:04:01.000000000 +0200
@@ -27,9 +27,8 @@

 my($seq, $name) = ('', '');
 my($lineNum, $l, $newName);
-#---
+
 # Read fasta file
-#---
 for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) {
        if( $l =~/^>\s*(.*?)\s+.*/ ) {
                $newName = $1;
Only in snpEff-5.0/scripts: make_and_commit_docs.sh
diff -ru snpEff-5.0.old/scripts/snpEff snpEff-5.0/scripts/snpEff
--- snpEff-5.0.old/scripts/snpEff       2020-08-10 03:24:23.000000000 +0200
+++ snpEff-5.0/scripts/snpEff   2020-10-04 22:04:01.000000000 +0200
@@ -5,7 +5,7 @@
 # Wrapper for HomeBrew-science project
 #
 # snpEff executable shell script
-# http://snpeff.sourceforge.net/
+# https://pcingola.github.io/SnpEff/
 # Extracts memory and system property Java arguments from the list of provided arguments
 # (ie -Xms 1g -Xmx 4g)
 #
diff -ru snpEff-5.0.old/snpEff.config snpEff-5.0/snpEff.config
--- snpEff-5.0.old/snpEff.config        2020-08-10 03:24:23.000000000 +0200
+++ snpEff-5.0/snpEff.config    2020-10-04 22:04:01.000000000 +0200
@@ -25,7 +25,7 @@
 #---
 # Latest version numbers. Check here if there is an update.
 #---
-#versions.url = http://snpeff.sourceforge.net/versions.txt
+#versions.url = https://pcingola.github.io/SnpEff/versions.txt
 versions.url = https://snpeff.blob.core.windows.net/databases/versions.txt

 #-------------------------------------------------------------------------------
@@ -183,10 +183,10 @@
        GRCh37.p13.RefSeq.MT.codonTable : Vertebrate_Mitochondrial

 # GRCh38 release from NCBI's RefSeq
-GRCh38.p7.RefSeq.genome : Human genome GRCh38 using RefSeq transcripts
-GRCh38.p7.RefSeq.reference : ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/
-       GRCh38.p7.RefSeq.M.codonTable : Vertebrate_Mitochondrial
-       GRCh38.p7.RefSeq.MT.codonTable : Vertebrate_Mitochondrial
+GRCh38.p13.RefSeq.genome : Human genome GRCh38 using RefSeq transcripts
+GRCh38.p13.RefSeq.reference : ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/
+       GRCh38.p13.RefSeq.M.codonTable : Vertebrate_Mitochondrial
+       GRCh38.p13.RefSeq.MT.codonTable : Vertebrate_Mitochondrial

 # Mouse
 mm9.genome : Mouse
Binary files snpEff-5.0.old/snpEff.jar and snpEff-5.0/snpEff.jar differ
Binary files snpEff-5.0.old/SnpSift.jar and snpEff-5.0/SnpSift.jar differ

boegel · 2021-06-05T19:25:08Z

@boegelbot please test @ generoso

boegelbot · 2021-06-05T19:30:10Z

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=13062 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_13062 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 17372

Test results coming soon (I hope)...

- notification for comment with ID 855284719 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2021-06-05T19:30:33Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
generoso-c1-s-1 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/3ffcc5d88445b9c2281972b8c7d6e3bc for a full test report.

boegel · 2021-06-05T19:34:56Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (1 easyconfigs in total)
node3154.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/8d7cdbdbb573631ca6dcfd50581c15f9 for a full test report.

verdurin · 2021-06-07T12:15:03Z

Test report by @verdurin
SUCCESS
Build succeeded for 3 out of 3 (1 easyconfigs in total)
nuc.lan - Linux Fedora 33, x86_64, Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz, Python 3.9.4
See https://gist.github.com/582e64dea3d76e1b31f48cbef9f50e21 for a full test report.

verdurin

Looks fine.

verdurin · 2021-06-07T12:17:15Z

Going in, thanks @boegel!

fix checksum for snpEff 5.0

a7d99f4

boegel added the bug fix label Jun 5, 2021

boegel added this to the next release (4.4.1) milestone Jun 5, 2021

verdurin approved these changes Jun 7, 2021

View reviewed changes

verdurin merged commit 19239c5 into easybuilders:develop Jun 7, 2021

boegel deleted the 20210605212315_new_pr_snpEff50 branch June 7, 2021 16:11

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fix checksum for snpEff 5.0 #13062

fix checksum for snpEff 5.0 #13062

boegel commented Jun 5, 2021 •

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verdurin commented Jun 7, 2021

fix checksum for snpEff 5.0 #13062

fix checksum for snpEff 5.0 #13062

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verdurin commented Jun 7, 2021

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