Warning
Iceberg was decommissioned on 30th November 2020. Users of Iceberg need to switch to using ShARC and/or Bessemer instead.
SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
After connecting to Iceberg (see Establishing a SSH connection), start an interactive session with the qsh
command.
Next, load a specific version of Samtools with one of the following:
module load apps/gcc/6.2/samtools/1.3.1
module load apps/gcc/5.2/samtools/1.2
This command makes the Samtools binary directory available to your session.
Once you have made Samtools available to the system using the module
command above, you can read the man pages by typing
man samtools
This section is primarily for system administrators.
Version 1.3.1
Built Samtools plus the bundled HTSlib, HTSlib utilities such as bgzip
plus various useful plugins. Compiled using GCC 6.2 (GNU Compiler Collection (gcc)).
Ran all tests using make tests
; a summary of the results is shown below; for full results see /usr/local/packages6/apps/gcc/6.2/samtools/1.3.1/tests.log
Number of tests:
total .. 423
passed .. 403
failed .. 0
expected failure .. 20
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
cd test/mpileup && ./regression.sh mpileup.reg
=== Testing mpileup.reg regressions ===
Expected passes: 124
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
=> PASS
cd test/mpileup && ./regression.sh depth.reg
=== Testing depth.reg regressions ===
Expected passes: 14
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
=> PASS
Installed Samtools to /usr/local/packages6/apps/gcc/6.2/samtools/1.3.1
Next, this modulefile
was installed as /usr/local/modulefiles/apps/gcc/6.2/samtools/1.3.1
Version 1.2
Installed using GCC 5.2 (GNU Compiler Collection (gcc))
module load compilers/gcc/5.2
tar -xvjf ./samtools-1.2.tar.bz2
cd samtools-1.2
mkdir -p /usr/local/packages6/apps/gcc/5.2/samtools/1.2
make prefix=/usr/local/packages6/apps/gcc/5.2/samtools/1.2
make prefix=/usr/local/packages6/apps/gcc/5.2/samtools/1.2 install
#tabix and bgzip are not installed by the above procedure.
#We can get them by doing the following
cd htslib-1.2.1/
make
mv ./tabix /usr/local/packages6/apps/gcc/5.2/samtools/1.2/bin/
mv ./bgzip /usr/local/packages6/apps/gcc/5.2/samtools/1.2/bin/
The test suite was run with
make test 2>&1 | tee make_tests.log
The summary of the test output was
Test output:
Number of tests:
total .. 368
passed .. 336
failed .. 0
expected failure .. 32
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
test/merge/test_pretty_header
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
cd test/mpileup && ./regression.sh
Samtools mpileup tests:
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|awk '{print $4}'
Expected passes: 123
Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
The full log is on the system at /usr/local/packages6/apps/gcc/5.2/samtools/1.2/make_tests.log
This modulefile
was installed as /usr/local/modulefiles/apps/gcc/5.2/samtools/1.2